rs1553318

Variant names:

• chr5-157052312-G-A
• rs1553318
• NM_001173393.3:c.673+49C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-157052312-G-A
• chr5-157052312-G-C
• chr5-157052312-G-T

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_001173393.3(HAVCR1):​c.673+49C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00925 in 1,544,842 control chromosomes in the GnomAD database, including 92 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0070 (4 hom., cov: 32)
  • Exomes 𝑓: 0.0095 (88 hom.)
• Consequence: HAVCR1 NM_001173393.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.209
• Publications: 26 publications found

Genes affected

HAVCR1 (HGNC:17866): (hepatitis A virus cellular receptor 1) The protein encoded by this gene is a membrane receptor for both human hepatitis A virus (HHAV) and TIMD4. The encoded protein may be involved in the moderation of asthma and allergic diseases. The reference genome represents an allele that retains a MTTVP amino acid segment that confers protection against atopy in HHAV seropositive individuals. The protein is a receptor for multiple other viruses, including Ebola virus, Marburg virus, Dengue virus, and Zika virus and is a possible entry factor for SARS-CoV-2 and other coronaviruses. [provided by RefSeq, Sep 2021]

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BS2: High Homozygotes in GnomAd4 at 4 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001173393.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HAVCR1	NM_001173393.3	MANE Select	c.673+49C>T		intron	N/A	NP_001166864.1	Q96D42
	HAVCR1	NM_001308156.2		c.673+49C>T		intron	N/A	NP_001295085.1	E9PFX0
	HAVCR1	NM_012206.3		c.673+49C>T		intron	N/A	NP_036338.2	B4DPB1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HAVCR1	ENST00000523175.6	TSL:1 MANE Select	c.673+49C>T		intron	N/A	ENSP00000427898.1	Q96D42
	HAVCR1	ENST00000339252.8	TSL:1	c.673+49C>T		intron	N/A	ENSP00000344844.3	Q96D42
	HAVCR1	ENST00000522693.5	TSL:2	c.673+49C>T		intron	N/A	ENSP00000428524.1	E9PFX0

Frequencies

GnomAD3 genomes AF: 0.00697 AC: 1060 AN: 152018 Hom.: 4 Cov.: 32

Gnomad AFR AF: 0.00244

Gnomad AMI AF: 0.0484

Gnomad AMR AF: 0.00590

Gnomad ASJ AF: 0.00547

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00103

Gnomad FIN AF: 0.00397

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0110

Gnomad OTH AF: 0.00431

GnomAD2 exomes AF: 0.00621 AC: 1504 AN: 241998 AF XY: 0.00622

Gnomad AFR exome AF: 0.00208

Gnomad AMR exome AF: 0.00416

Gnomad ASJ exome AF: 0.00215

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00448

Gnomad NFE exome AF: 0.0106

Gnomad OTH exome AF: 0.00509

GnomAD4 exome AF: 0.00950 AC: 13234 AN: 1392706 Hom.: 88 Cov.: 22 AF XY: 0.00933 AC XY: 6493 AN XY: 695890

African (AFR) AF: 0.00175 AC: 56 AN: 31932

American (AMR) AF: 0.00440 AC: 195 AN: 44290

Ashkenazi Jewish (ASJ) AF: 0.00303 AC: 76 AN: 25088

East Asian (EAS) AF: 0.00 AC: 0 AN: 39402

South Asian (SAS) AF: 0.000790 AC: 66 AN: 83522

European-Finnish (FIN) AF: 0.00486 AC: 258 AN: 53054

Middle Eastern (MID) AF: 0.000710 AC: 4 AN: 5630

European-Non Finnish (NFE) AF: 0.0115 AC: 12136 AN: 1051876

Other (OTH) AF: 0.00765 AC: 443 AN: 57912

GnomAD4 genome AF: 0.00696 AC: 1059 AN: 152136 Hom.: 4 Cov.: 32 AF XY: 0.00610 AC XY: 454 AN XY: 74368

African (AFR) AF: 0.00243 AC: 101 AN: 41500

American (AMR) AF: 0.00583 AC: 89 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.00547 AC: 19 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5170

South Asian (SAS) AF: 0.00104 AC: 5 AN: 4830

European-Finnish (FIN) AF: 0.00397 AC: 42 AN: 10578

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0110 AC: 749 AN: 67996

Other (OTH) AF: 0.00427 AC: 9 AN: 2110

Alfa AF: 0.00571 Hom.: 3103

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.42
DANN	Benign	0.33
PhyloP100		-0.21
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1553318; hg19: chr5-156479323;