chr4-125053663-C-T

Variant names:

• chr4-125053663-C-T
• rs2710818

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 0.69 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
• Publications: 2 publications found

ACMG classification

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

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

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.717 AC: 29749 AN: 41474

American (AMR) AF: 0.593 AC: 9020 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.677 AC: 2345 AN: 3462

East Asian (EAS) AF: 0.440 AC: 2267 AN: 5154

South Asian (SAS) AF: 0.542 AC: 2608 AN: 4814

European-Finnish (FIN) AF: 0.620 AC: 6519 AN: 10518

Middle Eastern (MID) AF: 0.666 AC: 193 AN: 290

European-Non Finnish (NFE) AF: 0.736 AC: 49998 AN: 67892

Other (OTH) AF: 0.706 AC: 1484 AN: 2102

Alfa AF: 0.701 Hom.: 34863

Bravo AF: 0.688

Asia WGS AF: 0.516 AC: 1778 AN: 3442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.33
DANN	Benign	0.46
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs2710818; hg19: chr4-125974818;