chr3-127101845-T-C

Variant names:

• chr3-127101845-T-C
• rs13066695

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 0.411 in 150,772 control chromosomes in the GnomAD database, including 13,075 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 0.41 (13075 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295
• Publications: 2 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 (EAS) allele frequency at 95% confidence interval = 0.547 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: 0.410 AC: 61834 AN: 150652 Hom.: 13053 Cov.: 30

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.306

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.411 AC: 61909 AN: 150772 Hom.: 13075 Cov.: 30 AF XY: 0.415 AC XY: 30558 AN XY: 73664

African (AFR) AF: 0.515 AC: 21116 AN: 41000

American (AMR) AF: 0.301 AC: 4563 AN: 15138

Ashkenazi Jewish (ASJ) AF: 0.360 AC: 1244 AN: 3456

East Asian (EAS) AF: 0.564 AC: 2856 AN: 5064

South Asian (SAS) AF: 0.500 AC: 2377 AN: 4754

European-Finnish (FIN) AF: 0.414 AC: 4330 AN: 10470

Middle Eastern (MID) AF: 0.285 AC: 81 AN: 284

European-Non Finnish (NFE) AF: 0.359 AC: 24274 AN: 67614

Other (OTH) AF: 0.379 AC: 793 AN: 2090

Alfa AF: 0.363 Hom.: 23386

Bravo AF: 0.402

Asia WGS AF: 0.560 AC: 1944 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	0.28
DANN	Benign	0.40
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs13066695; hg19: chr3-126820688;