7-96768437-T-C

Variant names:

• chr7-96768437-T-C
• rs1449591

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 0.745 in 152,112 control chromosomes in the GnomAD database, including 43,556 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 (43556 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.116
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.85 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: 0.745 AC: 113265 AN: 151994 Hom.: 43546 Cov.: 32

Gnomad AFR AF: 0.569

Gnomad AMI AF: 0.907

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.782

Gnomad EAS AF: 0.662

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.856

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.856

Gnomad OTH AF: 0.751

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

GnomAD4 genome AF: 0.745 AC: 113309 AN: 152112 Hom.: 43556 Cov.: 32 AF XY: 0.741 AC XY: 55077 AN XY: 74358

African (AFR) AF: 0.569 AC: 23601 AN: 41466

American (AMR) AF: 0.693 AC: 10575 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.782 AC: 2715 AN: 3472

East Asian (EAS) AF: 0.662 AC: 3425 AN: 5174

South Asian (SAS) AF: 0.645 AC: 3108 AN: 4816

European-Finnish (FIN) AF: 0.856 AC: 9067 AN: 10590

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.856 AC: 58202 AN: 68006

Other (OTH) AF: 0.742 AC: 1568 AN: 2112

Alfa AF: 0.825 Hom.: 38985

Bravo AF: 0.727

Asia WGS AF: 0.613 AC: 2135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.5
DANN	Benign	0.66
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs1449591; hg19: chr7-96397749;