rs1073690

Positions:

• chr4-95876752-C-A
• chr4-95876752-C-G
• chr4-95876752-C-T

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 0.949 in 151,448 control chromosomes in the GnomAD database, including 68,269 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 0.95 (68269 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.177

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.95876752C>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.949 AC: 143633 AN: 151330 Hom.: 68213 Cov.: 32

Gnomad AFR AF: 0.970

Gnomad AMI AF: 0.964

Gnomad AMR AF: 0.948

Gnomad ASJ AF: 0.939

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.953

Gnomad FIN AF: 0.973

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.929

Gnomad OTH AF: 0.949

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

GnomAD4 genome AF: 0.949 AC: 143748 AN: 151448 Hom.: 68269 Cov.: 32 AF XY: 0.951 AC XY: 70391 AN XY: 73996

Gnomad4 AFR AF: 0.970

Gnomad4 AMR AF: 0.949

Gnomad4 ASJ AF: 0.939

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.953

Gnomad4 FIN AF: 0.973

Gnomad4 NFE AF: 0.929

Gnomad4 OTH AF: 0.950

Alfa AF: 0.939 Hom.: 12395

Bravo AF: 0.949

Asia WGS AF: 0.977 AC: 3399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.1
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1073690; hg19: chr4-96797903;