7-155068525-C-T

Variant names:

• chr7-155068525-C-T
• rs2873379
• ENST00000395731.5:n.1245G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000395731.5(HTR5A-AS1):​n.1245G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.706 in 152,118 control chromosomes in the GnomAD database, including 38,107 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 0.71 (38107 hom., cov: 32)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: HTR5A-AS1 ENST00000395731.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86
• Publications: 1 publications found

Genes affected

HTR5A-AS1 (HGNC:48956): (HTR5A antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000395731.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HTR5A-AS1	NR_038945.1		n.1245G>A		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HTR5A-AS1	ENST00000395731.5	TSL:1	n.1245G>A		non_coding_transcript_exon	Exon 2 of 2
	HTR5A-AS1	ENST00000655797.2		n.1570G>A		non_coding_transcript_exon	Exon 3 of 3
	HTR5A-AS1	ENST00000671665.1		n.2138G>A		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.706 AC: 107307 AN: 151996 Hom.: 38074 Cov.: 32

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.769

Gnomad ASJ AF: 0.780

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.734

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.723

Gnomad OTH AF: 0.720

GnomAD4 exome AF: 0.250 AC: 1 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.250 AC: 1 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.706 AC: 107398 AN: 152114 Hom.: 38107 Cov.: 32 AF XY: 0.709 AC XY: 52691 AN XY: 74362

African (AFR) AF: 0.652 AC: 27050 AN: 41484

American (AMR) AF: 0.768 AC: 11744 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.780 AC: 2709 AN: 3472

East Asian (EAS) AF: 0.591 AC: 3058 AN: 5174

South Asian (SAS) AF: 0.749 AC: 3611 AN: 4820

European-Finnish (FIN) AF: 0.734 AC: 7763 AN: 10572

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.723 AC: 49144 AN: 67990

Other (OTH) AF: 0.722 AC: 1523 AN: 2110

Alfa AF: 0.721 Hom.: 25782

Bravo AF: 0.703

Asia WGS AF: 0.693 AC: 2408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.4
DANN	Benign	0.52
PhyloP100		-1.9
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2873379; hg19: chr7-154860235;