2-7247316-C-T

Variant names:

• chr2-7247316-C-T
• rs2140855

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.501

Gnomad4 AMR AF: 0.587

Gnomad4 ASJ AF: 0.643

Gnomad4 EAS AF: 0.515

Gnomad4 SAS AF: 0.703

Gnomad4 FIN AF: 0.732

Gnomad4 NFE AF: 0.628

Gnomad4 OTH AF: 0.597

Alfa AF: 0.621 Hom.: 39696

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2140855; hg19: chr2-7387447;