rs1565198

Variant names:

• chr5-8155141-A-C
• rs1565198
• ENST00000830491.1:n.214-18214A>C

Your query was ambiguous. Multiple possible variants found:

• chr5-8155141-A-C
• chr5-8155141-A-T

Variant summary

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

The ENST00000830491.1(ENSG00000308020):​n.214-18214A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.442 in 152,020 control chromosomes in the GnomAD database, including 16,225 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 0.44 (16225 hom., cov: 32)
• Consequence: ENSG00000308020 ENST00000830491.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0850
• Publications: 3 publications found

Genes affected

ENSG00000308020 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.675 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308020	ENST00000830491.1	n.214-18214A>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.442 AC: 67121 AN: 151902 Hom.: 16219 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.694

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.461

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.442 AC: 67150 AN: 152020 Hom.: 16225 Cov.: 32 AF XY: 0.447 AC XY: 33210 AN XY: 74326

African (AFR) AF: 0.235 AC: 9732 AN: 41488

American (AMR) AF: 0.540 AC: 8239 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1564 AN: 3470

East Asian (EAS) AF: 0.693 AC: 3581 AN: 5164

South Asian (SAS) AF: 0.580 AC: 2794 AN: 4820

European-Finnish (FIN) AF: 0.480 AC: 5053 AN: 10532

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.509 AC: 34571 AN: 67970

Other (OTH) AF: 0.465 AC: 982 AN: 2112

Alfa AF: 0.474 Hom.: 8866

Bravo AF: 0.441

Asia WGS AF: 0.591 AC: 2051 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.2
DANN	Benign	0.62
PhyloP100		-0.085

Splicing

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

Other links and lift over

dbSNP: rs1565198; hg19: chr5-8155254;