chr2-116716206-T-C

Variant names:

• chr2-116716206-T-C
• rs7584028

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 0.472 in 151,882 control chromosomes in the GnomAD database, including 17,192 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 0.47 (17192 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.391
• Publications: 1 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 (NFE) allele frequency at 95% confidence interval = 0.488 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: 0.472 AC: 71689 AN: 151764 Hom.: 17189 Cov.: 32

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.472 AC: 71712 AN: 151882 Hom.: 17192 Cov.: 32 AF XY: 0.470 AC XY: 34850 AN XY: 74226

African (AFR) AF: 0.482 AC: 19979 AN: 41438

American (AMR) AF: 0.381 AC: 5800 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1561 AN: 3470

East Asian (EAS) AF: 0.352 AC: 1806 AN: 5128

South Asian (SAS) AF: 0.380 AC: 1834 AN: 4824

European-Finnish (FIN) AF: 0.519 AC: 5477 AN: 10556

Middle Eastern (MID) AF: 0.418 AC: 122 AN: 292

European-Non Finnish (NFE) AF: 0.493 AC: 33464 AN: 67918

Other (OTH) AF: 0.485 AC: 1022 AN: 2106

Alfa AF: 0.474 Hom.: 2153

Bravo AF: 0.463

Asia WGS AF: 0.379 AC: 1317 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	6.3
DANN	Benign	0.71
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs7584028; hg19: chr2-117473782;