2-6461776-T-C

Variant names:

• chr2-6461776-T-C
• rs7593230

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 0.537 in 151,746 control chromosomes in the GnomAD database, including 22,438 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 0.54 (22438 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.682
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.687 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: 0.537 AC: 81441 AN: 151626 Hom.: 22419 Cov.: 31

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.537 AC: 81520 AN: 151746 Hom.: 22438 Cov.: 31 AF XY: 0.547 AC XY: 40588 AN XY: 74156

African (AFR) AF: 0.590 AC: 24446 AN: 41402

American (AMR) AF: 0.579 AC: 8824 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1393 AN: 3470

East Asian (EAS) AF: 0.707 AC: 3650 AN: 5166

South Asian (SAS) AF: 0.557 AC: 2681 AN: 4816

European-Finnish (FIN) AF: 0.678 AC: 7124 AN: 10502

Middle Eastern (MID) AF: 0.314 AC: 91 AN: 290

European-Non Finnish (NFE) AF: 0.468 AC: 31730 AN: 67842

Other (OTH) AF: 0.495 AC: 1040 AN: 2100

Alfa AF: 0.504 Hom.: 2369

Bravo AF: 0.532

Asia WGS AF: 0.648 AC: 2235 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.5
DANN	Benign	0.89
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs7593230; hg19: chr2-6601908;