chr2-7221149-T-C

Variant names:

• chr2-7221149-T-C
• rs11682769

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 0.354 in 152,062 control chromosomes in the GnomAD database, including 10,028 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 0.35 (10028 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.414
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.439 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: 0.354 AC: 53740 AN: 151942 Hom.: 9998 Cov.: 32

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.354 AC: 53802 AN: 152062 Hom.: 10028 Cov.: 32 AF XY: 0.356 AC XY: 26470 AN XY: 74340

African (AFR) AF: 0.444 AC: 18431 AN: 41476

American (AMR) AF: 0.251 AC: 3829 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.292 AC: 1010 AN: 3462

East Asian (EAS) AF: 0.137 AC: 708 AN: 5180

South Asian (SAS) AF: 0.360 AC: 1738 AN: 4822

European-Finnish (FIN) AF: 0.460 AC: 4870 AN: 10578

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 22051 AN: 67972

Other (OTH) AF: 0.343 AC: 724 AN: 2108

Alfa AF: 0.325 Hom.: 33969

Bravo AF: 0.339

Asia WGS AF: 0.283 AC: 984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.4
DANN	Benign	0.69
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs11682769; hg19: chr2-7361280;