rs4695138

Variant names:

• chr4-45954163-A-T
• rs4695138

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 0.377 in 151,958 control chromosomes in the GnomAD database, including 11,861 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 0.38 (11861 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.301
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.455 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: 0.377 AC: 57213 AN: 151840 Hom.: 11861 Cov.: 31

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.0235

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.377 AC: 57247 AN: 151958 Hom.: 11861 Cov.: 31 AF XY: 0.374 AC XY: 27802 AN XY: 74256

African (AFR) AF: 0.253 AC: 10494 AN: 41476

American (AMR) AF: 0.378 AC: 5762 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1584 AN: 3464

East Asian (EAS) AF: 0.0236 AC: 122 AN: 5178

South Asian (SAS) AF: 0.299 AC: 1437 AN: 4806

European-Finnish (FIN) AF: 0.480 AC: 5066 AN: 10546

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.460 AC: 31208 AN: 67916

Other (OTH) AF: 0.404 AC: 853 AN: 2110

Alfa AF: 0.415 Hom.: 1703

Bravo AF: 0.364

Asia WGS AF: 0.150 AC: 526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.4
DANN	Benign	0.67
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs4695138; hg19: chr4-45956180;