7-86643624-C-T

Variant names:

• chr7-86643624-C-T
• rs274622

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 0.677 in 151,944 control chromosomes in the GnomAD database, including 35,112 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 0.68 (35112 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.739

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.857 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: 0.677 AC: 102731 AN: 151826 Hom.: 35058 Cov.: 30

Gnomad AFR AF: 0.660

Gnomad AMI AF: 0.700

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.682

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.669

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

GnomAD4 genome AF: 0.677 AC: 102839 AN: 151944 Hom.: 35112 Cov.: 30 AF XY: 0.681 AC XY: 50547 AN XY: 74230

Gnomad4 AFR AF: 0.661

Gnomad4 AMR AF: 0.742

Gnomad4 ASJ AF: 0.700

Gnomad4 EAS AF: 0.879

Gnomad4 SAS AF: 0.856

Gnomad4 FIN AF: 0.623

Gnomad4 NFE AF: 0.651

Gnomad4 OTH AF: 0.673

Alfa AF: 0.650 Hom.: 4847

Bravo AF: 0.684

Asia WGS AF: 0.848 AC: 2947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.8
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs274622; hg19: chr7-86272940;