chr3-172440607-T-C

Variant names:

• chr3-172440607-T-C
• rs1403637

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 0.297 in 152,080 control chromosomes in the GnomAD database, including 8,002 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 0.30 (8002 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.397 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: 0.297 AC: 45172 AN: 151962 Hom.: 8005 Cov.: 31

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.297 AC: 45160 AN: 152080 Hom.: 8002 Cov.: 31 AF XY: 0.293 AC XY: 21753 AN XY: 74340

African (AFR) AF: 0.120 AC: 4991 AN: 41528

American (AMR) AF: 0.299 AC: 4561 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.461 AC: 1598 AN: 3468

East Asian (EAS) AF: 0.192 AC: 992 AN: 5172

South Asian (SAS) AF: 0.217 AC: 1046 AN: 4822

European-Finnish (FIN) AF: 0.339 AC: 3573 AN: 10552

Middle Eastern (MID) AF: 0.459 AC: 134 AN: 292

European-Non Finnish (NFE) AF: 0.401 AC: 27265 AN: 67958

Other (OTH) AF: 0.347 AC: 732 AN: 2108

Alfa AF: 0.372 Hom.: 44850

Bravo AF: 0.287

Asia WGS AF: 0.181 AC: 634 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.10
DANN	Benign	0.68
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1403637; hg19: chr3-172158397;