rs2710818

chr4-125053663-C-T

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 0.69 in 151,822 control chromosomes in the GnomAD database, including 36,716 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 0.69 (36716 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.470

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.731 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104741 AN: 151706 Hom.: 36691 Cov.: 32

Gnomad AFR AF: 0.717

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.620

Gnomad MID AF: 0.673

Gnomad NFE AF: 0.736

Gnomad OTH AF: 0.707

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

GnomAD4 genome AF: 0.690 AC: 104813 AN: 151822 Hom.: 36716 Cov.: 32 AF XY: 0.678 AC XY: 50307 AN XY: 74170

Gnomad4 AFR AF: 0.717

Gnomad4 AMR AF: 0.593

Gnomad4 ASJ AF: 0.677

Gnomad4 EAS AF: 0.440

Gnomad4 SAS AF: 0.542

Gnomad4 FIN AF: 0.620

Gnomad4 NFE AF: 0.736

Gnomad4 OTH AF: 0.706

Alfa AF: 0.699 Hom.: 17098

Bravo AF: 0.688

Asia WGS AF: 0.516 AC: 1778 AN: 3442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.33
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2710818; hg19: chr4-125974818;