rs17302632

Variant names:

• chr1-181070392-C-T
• rs17302632
• ENST00000826164.1:n.88+335G>A

Variant summary

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

The ENST00000826164.1(ENSG00000307418):​n.88+335G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0426 in 152,326 control chromosomes in the GnomAD database, including 172 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 0.043 (172 hom., cov: 32)
• Consequence: ENSG00000307418 ENST00000826164.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0620
• Publications: 4 publications found

Genes affected

ENSG00000307418 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0562 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
ENSG00000307418	ENST00000826164.1	n.88+335G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0426 AC: 6480 AN: 152208 Hom.: 171 Cov.: 32

Gnomad AFR AF: 0.0278

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0394

Gnomad ASJ AF: 0.0816

Gnomad EAS AF: 0.0620

Gnomad SAS AF: 0.0521

Gnomad FIN AF: 0.0437

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0479

Gnomad OTH AF: 0.0521

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

GnomAD4 genome AF: 0.0426 AC: 6482 AN: 152326 Hom.: 172 Cov.: 32 AF XY: 0.0413 AC XY: 3079 AN XY: 74498

African (AFR) AF: 0.0278 AC: 1154 AN: 41576

American (AMR) AF: 0.0395 AC: 604 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0816 AC: 283 AN: 3470

East Asian (EAS) AF: 0.0618 AC: 320 AN: 5178

South Asian (SAS) AF: 0.0526 AC: 254 AN: 4830

European-Finnish (FIN) AF: 0.0437 AC: 464 AN: 10622

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0479 AC: 3258 AN: 68032

Other (OTH) AF: 0.0520 AC: 110 AN: 2114

Alfa AF: 0.0483 Hom.: 267

Bravo AF: 0.0426

Asia WGS AF: 0.0560 AC: 195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.9
DANN	Benign	0.71
PhyloP100		-0.062

Splicing

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

Other links and lift over

dbSNP: rs17302632; hg19: chr1-181039528;