3-172469163-T-C

Variant names:

• chr3-172469163-T-C
• rs10513702

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 0.49 in 151,922 control chromosomes in the GnomAD database, including 18,380 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 0.49 (18380 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.522
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.545 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: 0.490 AC: 74442 AN: 151804 Hom.: 18373 Cov.: 32

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.490 AC: 74489 AN: 151922 Hom.: 18380 Cov.: 32 AF XY: 0.490 AC XY: 36408 AN XY: 74240

African (AFR) AF: 0.455 AC: 18842 AN: 41386

American (AMR) AF: 0.459 AC: 7025 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.509 AC: 1766 AN: 3472

East Asian (EAS) AF: 0.502 AC: 2598 AN: 5172

South Asian (SAS) AF: 0.562 AC: 2714 AN: 4826

European-Finnish (FIN) AF: 0.512 AC: 5384 AN: 10516

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.508 AC: 34498 AN: 67938

Other (OTH) AF: 0.503 AC: 1064 AN: 2114

Alfa AF: 0.500 Hom.: 13679

Bravo AF: 0.483

Asia WGS AF: 0.549 AC: 1905 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.5
DANN	Benign	0.45
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs10513702; hg19: chr3-172186953;