3-127071607-T-G

Variant names:

• chr3-127071607-T-G
• rs11928855

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 0.358 in 152,048 control chromosomes in the GnomAD database, including 11,168 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 0.36 (11168 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.212
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.555 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: 0.358 AC: 54351 AN: 151930 Hom.: 11145 Cov.: 33

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.358 AC: 54404 AN: 152048 Hom.: 11168 Cov.: 33 AF XY: 0.359 AC XY: 26665 AN XY: 74314

African (AFR) AF: 0.561 AC: 23271 AN: 41458

American (AMR) AF: 0.352 AC: 5387 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 790 AN: 3468

East Asian (EAS) AF: 0.508 AC: 2617 AN: 5148

South Asian (SAS) AF: 0.328 AC: 1584 AN: 4826

European-Finnish (FIN) AF: 0.270 AC: 2855 AN: 10572

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16928 AN: 67972

Other (OTH) AF: 0.313 AC: 662 AN: 2114

Alfa AF: 0.265 Hom.: 2140

Bravo AF: 0.372

Asia WGS AF: 0.415 AC: 1443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.3
DANN	Benign	0.60
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs11928855; hg19: chr3-126790450; COSMIC: COSV68250920;