2-207641155-T-C

Variant names:

• chr2-207641155-T-C
• rs7594560

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 0.188 in 152,146 control chromosomes in the GnomAD database, including 3,172 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 0.19 (3172 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0760

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.299 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: 0.188 AC: 28610 AN: 152028 Hom.: 3167 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.188 AC: 28646 AN: 152146 Hom.: 3172 Cov.: 32 AF XY: 0.190 AC XY: 14107 AN XY: 74394

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.164

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.198

Alfa AF: 0.138 Hom.: 2255

Bravo AF: 0.202

Asia WGS AF: 0.218 AC: 757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.4
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7594560; hg19: chr2-208505879;