rs4626515

Variant names:

• chr7-140204330-T-C
• rs4626515

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 0.208 in 152,010 control chromosomes in the GnomAD database, including 5,154 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 0.21 (5154 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.411

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.453 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: 0.208 AC: 31607 AN: 151892 Hom.: 5141 Cov.: 31

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0238

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.208 AC: 31671 AN: 152010 Hom.: 5154 Cov.: 31 AF XY: 0.204 AC XY: 15125 AN XY: 74310

Gnomad4 AFR AF: 0.458

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0244

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.170

Alfa AF: 0.132 Hom.: 2231

Bravo AF: 0.224

Asia WGS AF: 0.0360 AC: 126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.82
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4626515; hg19: chr7-139904130;