rs4694317

Variant names:

• chr4-70485719-C-A
• rs4694317

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 0.349 in 151,888 control chromosomes in the GnomAD database, including 9,895 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 0.35 (9895 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.204
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.429 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: 0.349 AC: 52990 AN: 151770 Hom.: 9892 Cov.: 30

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.349 AC: 53005 AN: 151888 Hom.: 9895 Cov.: 30 AF XY: 0.346 AC XY: 25696 AN XY: 74210

African (AFR) AF: 0.227 AC: 9392 AN: 41454

American (AMR) AF: 0.437 AC: 6671 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 971 AN: 3470

East Asian (EAS) AF: 0.221 AC: 1138 AN: 5150

South Asian (SAS) AF: 0.262 AC: 1261 AN: 4808

European-Finnish (FIN) AF: 0.411 AC: 4322 AN: 10514

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.415 AC: 28187 AN: 67936

Other (OTH) AF: 0.364 AC: 766 AN: 2104

Alfa AF: 0.387 Hom.: 37303

Bravo AF: 0.346

Asia WGS AF: 0.252 AC: 876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.40
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs4694317; hg19: chr4-71351436;