rs2595085

Variant names:

• chr4-110715617-G-C
• rs2595085

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 0.607 in 151,798 control chromosomes in the GnomAD database, including 28,438 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 0.61 (28438 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.181
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.671 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: 0.607 AC: 92058 AN: 151680 Hom.: 28431 Cov.: 30

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.775

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.607 AC: 92104 AN: 151798 Hom.: 28438 Cov.: 30 AF XY: 0.595 AC XY: 44108 AN XY: 74154

African (AFR) AF: 0.537 AC: 22227 AN: 41392

American (AMR) AF: 0.590 AC: 8977 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.498 AC: 1730 AN: 3472

East Asian (EAS) AF: 0.414 AC: 2111 AN: 5098

South Asian (SAS) AF: 0.568 AC: 2733 AN: 4810

European-Finnish (FIN) AF: 0.586 AC: 6192 AN: 10566

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.677 AC: 45964 AN: 67932

Other (OTH) AF: 0.611 AC: 1285 AN: 2104

Alfa AF: 0.619 Hom.: 3626

Bravo AF: 0.605

Asia WGS AF: 0.474 AC: 1650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.61
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs2595085; hg19: chr4-111636773;