7-96811207-A-T

Variant names:

• chr7-96811207-A-T
• rs9655757

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 0.739 in 152,130 control chromosomes in the GnomAD database, including 44,736 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 0.74 (44736 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0120
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.891 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: 0.739 AC: 112388 AN: 152012 Hom.: 44711 Cov.: 32

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.744

Gnomad AMR AF: 0.837

Gnomad ASJ AF: 0.850

Gnomad EAS AF: 0.913

Gnomad SAS AF: 0.856

Gnomad FIN AF: 0.910

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.862

Gnomad OTH AF: 0.749

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

GnomAD4 genome AF: 0.739 AC: 112443 AN: 152130 Hom.: 44736 Cov.: 32 AF XY: 0.746 AC XY: 55483 AN XY: 74382

African (AFR) AF: 0.411 AC: 17060 AN: 41460

American (AMR) AF: 0.838 AC: 12803 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.850 AC: 2951 AN: 3472

East Asian (EAS) AF: 0.912 AC: 4708 AN: 5160

South Asian (SAS) AF: 0.857 AC: 4131 AN: 4820

European-Finnish (FIN) AF: 0.910 AC: 9652 AN: 10602

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.862 AC: 58653 AN: 68016

Other (OTH) AF: 0.752 AC: 1588 AN: 2112

Alfa AF: 0.788 Hom.: 6128

Bravo AF: 0.718

Asia WGS AF: 0.875 AC: 3040 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	2.7
DANN	Benign	0.46
PhyloP100		0.012

Splicing

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

Other links and lift over

dbSNP: rs9655757; hg19: chr7-96440519;