chr3-127068316-G-T

Variant names:

• chr3-127068316-G-T
• rs11921451

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 0.189 in 152,302 control chromosomes in the GnomAD database, including 3,382 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 0.19 (3382 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.262 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: 0.189 AC: 28808 AN: 152184 Hom.: 3381 Cov.: 34

Gnomad AFR AF: 0.0518

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.0963

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.189 AC: 28814 AN: 152302 Hom.: 3382 Cov.: 34 AF XY: 0.191 AC XY: 14184 AN XY: 74456

African (AFR) AF: 0.0517 AC: 2152 AN: 41592

American (AMR) AF: 0.170 AC: 2595 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 891 AN: 3472

East Asian (EAS) AF: 0.0966 AC: 500 AN: 5178

South Asian (SAS) AF: 0.265 AC: 1281 AN: 4830

European-Finnish (FIN) AF: 0.259 AC: 2751 AN: 10616

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 18045 AN: 68000

Other (OTH) AF: 0.188 AC: 396 AN: 2112

Alfa AF: 0.234 Hom.: 14744

Bravo AF: 0.175

Asia WGS AF: 0.186 AC: 648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.7
DANN	Benign	0.60
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs11921451; hg19: chr3-126787159;