7-95403792-C-G

Position:

• chr7-95403792-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0141 in 152,274 control chromosomes in the GnomAD database, including 35 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 0.014 (35 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.249

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0141 (2150/152274) while in subpopulation SAS AF= 0.0404 (195/4824). AF 95% confidence interval is 0.0358. There are 35 homozygotes in gnomad4. There are 1231 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 35 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.95403792C>G		intergenic_region
LOC107986822	XR_007060439.1	n.557+6764C>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0141 AC: 2152 AN: 152156 Hom.: 35 Cov.: 33

Gnomad AFR AF: 0.00198

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0115

Gnomad ASJ AF: 0.0190

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0402

Gnomad FIN AF: 0.0478

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0157

Gnomad OTH AF: 0.0153

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

GnomAD4 genome AF: 0.0141 AC: 2150 AN: 152274 Hom.: 35 Cov.: 33 AF XY: 0.0165 AC XY: 1231 AN XY: 74446

Gnomad4 AFR AF: 0.00197

Gnomad4 AMR AF: 0.0115

Gnomad4 ASJ AF: 0.0190

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0404

Gnomad4 FIN AF: 0.0478

Gnomad4 NFE AF: 0.0157

Gnomad4 OTH AF: 0.0151

Alfa AF: 0.0170 Hom.: 3

Bravo AF: 0.0103

Asia WGS AF: 0.0110 AC: 39 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.8
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17876205; hg19: chr7-95033104;