7-96768437-T-C

Position:

• chr7-96768437-T-C

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 0.745 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.116

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.96768437T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.569

Gnomad4 AMR AF: 0.693

Gnomad4 ASJ AF: 0.782

Gnomad4 EAS AF: 0.662

Gnomad4 SAS AF: 0.645

Gnomad4 FIN AF: 0.856

Gnomad4 NFE AF: 0.856

Gnomad4 OTH AF: 0.742

Alfa AF: 0.819 Hom.: 25410

Bravo AF: 0.727

Asia WGS AF: 0.613 AC: 2135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1449591; hg19: chr7-96397749;