chr7-96740301-C-A

Position:

• chr7-96740301-C-A

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 0.121 in 152,018 control chromosomes in the GnomAD database, including 1,098 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 0.12 (1098 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.131

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.96740301C>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18435 AN: 151900 Hom.: 1093 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.121 AC: 18458 AN: 152018 Hom.: 1098 Cov.: 32 AF XY: 0.123 AC XY: 9112 AN XY: 74276

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.127

Alfa AF: 0.121 Hom.: 284

Bravo AF: 0.122

Asia WGS AF: 0.148 AC: 516 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.0
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17167761; hg19: chr7-96369613;