7-89705354-T-G

Variant names:

• chr7-89705354-T-G
• rs2724463

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 0.669 in 152,046 control chromosomes in the GnomAD database, including 34,131 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 0.67 (34131 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.586
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.669 AC: 101605 AN: 151926 Hom.: 34100 Cov.: 33

Gnomad AFR AF: 0.617

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.670

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.685

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

GnomAD4 genome AF: 0.669 AC: 101696 AN: 152046 Hom.: 34131 Cov.: 33 AF XY: 0.672 AC XY: 49926 AN XY: 74326

African (AFR) AF: 0.617 AC: 25583 AN: 41442

American (AMR) AF: 0.709 AC: 10823 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.664 AC: 2303 AN: 3470

East Asian (EAS) AF: 0.670 AC: 3467 AN: 5178

South Asian (SAS) AF: 0.732 AC: 3522 AN: 4814

European-Finnish (FIN) AF: 0.694 AC: 7332 AN: 10566

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.681 AC: 46322 AN: 67988

Other (OTH) AF: 0.688 AC: 1450 AN: 2108

Alfa AF: 0.679 Hom.: 145655

Bravo AF: 0.666

Asia WGS AF: 0.696 AC: 2416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.9
DANN	Benign	0.47
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs2724463; hg19: chr7-89334668;