4-95876752-C-A

Variant names:

• chr4-95876752-C-A
• rs1073690

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.177
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.970 AC: 40197 AN: 41442

American (AMR) AF: 0.949 AC: 14359 AN: 15138

Ashkenazi Jewish (ASJ) AF: 0.939 AC: 3245 AN: 3454

East Asian (EAS) AF: 0.999 AC: 5096 AN: 5100

South Asian (SAS) AF: 0.953 AC: 4597 AN: 4824

European-Finnish (FIN) AF: 0.973 AC: 10332 AN: 10620

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.929 AC: 62784 AN: 67562

Other (OTH) AF: 0.950 AC: 1996 AN: 2102

Alfa AF: 0.941 Hom.: 23896

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
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs1073690; hg19: chr4-96797903;