chr7-86643624-C-T

Variant names:

• chr7-86643624-C-T
• rs274622

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 0.677 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
• Publications: 17 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.661 AC: 27373 AN: 41422

American (AMR) AF: 0.742 AC: 11332 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.700 AC: 2427 AN: 3468

East Asian (EAS) AF: 0.879 AC: 4545 AN: 5172

South Asian (SAS) AF: 0.856 AC: 4122 AN: 4818

European-Finnish (FIN) AF: 0.623 AC: 6566 AN: 10542

Middle Eastern (MID) AF: 0.668 AC: 195 AN: 292

European-Non Finnish (NFE) AF: 0.651 AC: 44222 AN: 67940

Other (OTH) AF: 0.673 AC: 1420 AN: 2110

Alfa AF: 0.662 Hom.: 49194

Bravo AF: 0.684

Asia WGS AF: 0.848 AC: 2947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.8
DANN	Benign	0.71
PhyloP100		-0.74
PromoterAI		-0.014	Neutral

Splicing

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

Other links and lift over

dbSNP: rs274622; hg19: chr7-86272940;