2-616686-T-C

Variant names:

• chr2-616686-T-C
• rs7571872

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 0.608 in 152,000 control chromosomes in the GnomAD database, including 28,341 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 0.61 (28341 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.636 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: 0.608 AC: 92411 AN: 151882 Hom.: 28336 Cov.: 33

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.608 AC: 92444 AN: 152000 Hom.: 28341 Cov.: 33 AF XY: 0.608 AC XY: 45141 AN XY: 74302

African (AFR) AF: 0.587 AC: 24311 AN: 41406

American (AMR) AF: 0.547 AC: 8348 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.582 AC: 2021 AN: 3472

East Asian (EAS) AF: 0.423 AC: 2187 AN: 5172

South Asian (SAS) AF: 0.548 AC: 2639 AN: 4820

European-Finnish (FIN) AF: 0.685 AC: 7236 AN: 10570

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.641 AC: 43603 AN: 67980

Other (OTH) AF: 0.613 AC: 1293 AN: 2108

Alfa AF: 0.541 Hom.: 3506

Bravo AF: 0.597

Asia WGS AF: 0.490 AC: 1704 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.49
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs7571872; hg19: chr2-616686;