chr1-102635356-C-T

Variant names:

• chr1-102635356-C-T
• rs1517432

Variant summary

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

The variant allele was found at a frequency of 0.472 in 151,906 control chromosomes in the GnomAD database, including 20,016 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 0.47 (20016 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.325
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.605 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

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71676 AN: 151788 Hom.: 20002 Cov.: 31

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.472 AC: 71693 AN: 151906 Hom.: 20016 Cov.: 31 AF XY: 0.481 AC XY: 35720 AN XY: 74216

African (AFR) AF: 0.153 AC: 6352 AN: 41470

American (AMR) AF: 0.615 AC: 9389 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1745 AN: 3468

East Asian (EAS) AF: 0.600 AC: 3077 AN: 5130

South Asian (SAS) AF: 0.541 AC: 2601 AN: 4806

European-Finnish (FIN) AF: 0.706 AC: 7448 AN: 10546

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.580 AC: 39381 AN: 67916

Other (OTH) AF: 0.484 AC: 1019 AN: 2106

Alfa AF: 0.499 Hom.: 2733

Bravo AF: 0.455

Asia WGS AF: 0.566 AC: 1962 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.85
DANN	Benign	0.31
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs1517432; hg19: chr1-103100912;