rs2595085

Positions:

• chr4-110715617-G-C

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 0.607 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.537

Gnomad4 AMR AF: 0.590

Gnomad4 ASJ AF: 0.498

Gnomad4 EAS AF: 0.414

Gnomad4 SAS AF: 0.568

Gnomad4 FIN AF: 0.586

Gnomad4 NFE AF: 0.677

Gnomad4 OTH AF: 0.611

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2595085; hg19: chr4-111636773;