chr2-7247316-C-T

Variant names:

• chr2-7247316-C-T
• rs2140855

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 0.594 in 152,106 control chromosomes in the GnomAD database, including 27,224 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 0.59 (27224 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.291
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.683 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: 0.594 AC: 90295 AN: 151988 Hom.: 27211 Cov.: 33

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.643

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.703

Gnomad FIN AF: 0.732

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.594

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

GnomAD4 genome AF: 0.594 AC: 90346 AN: 152106 Hom.: 27224 Cov.: 33 AF XY: 0.600 AC XY: 44621 AN XY: 74348

African (AFR) AF: 0.501 AC: 20789 AN: 41498

American (AMR) AF: 0.587 AC: 8973 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.643 AC: 2227 AN: 3466

East Asian (EAS) AF: 0.515 AC: 2655 AN: 5152

South Asian (SAS) AF: 0.703 AC: 3388 AN: 4820

European-Finnish (FIN) AF: 0.732 AC: 7748 AN: 10580

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.628 AC: 42701 AN: 67986

Other (OTH) AF: 0.597 AC: 1261 AN: 2114

Alfa AF: 0.616 Hom.: 49241

Bravo AF: 0.573

Asia WGS AF: 0.619 AC: 2151 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.91
DANN	Benign	0.53
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs2140855; hg19: chr2-7387447;