rs2110483

Positions:

• chr7-94250781-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 0.178 in 151,956 control chromosomes in the GnomAD database, including 4,592 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 0.18 (4592 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.938

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.94250781T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26929 AN: 151838 Hom.: 4573 Cov.: 32

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.0870

Gnomad EAS AF: 0.0455

Gnomad SAS AF: 0.0723

Gnomad FIN AF: 0.0270

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.0637

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.178 AC: 26994 AN: 151956 Hom.: 4592 Cov.: 32 AF XY: 0.172 AC XY: 12748 AN XY: 74272

Gnomad4 AFR AF: 0.451

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.0870

Gnomad4 EAS AF: 0.0455

Gnomad4 SAS AF: 0.0726

Gnomad4 FIN AF: 0.0270

Gnomad4 NFE AF: 0.0637

Gnomad4 OTH AF: 0.163

Alfa AF: 0.134 Hom.: 692

Bravo AF: 0.202

Asia WGS AF: 0.0970 AC: 339 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.55
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2110483; hg19: chr7-93880093;