rs10025456

Variant names:

• chr4-10138635-T-C
• rs10025456

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 0.464 in 152,170 control chromosomes in the GnomAD database, including 16,676 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 0.46 (16676 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31
• 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 (SAS) allele frequency at 95% confidence interval = 0.557 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: 0.464 AC: 70522 AN: 152052 Hom.: 16676 Cov.: 33

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.464 AC: 70544 AN: 152170 Hom.: 16676 Cov.: 33 AF XY: 0.466 AC XY: 34651 AN XY: 74404

African (AFR) AF: 0.428 AC: 17761 AN: 41508

American (AMR) AF: 0.381 AC: 5830 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1164 AN: 3470

East Asian (EAS) AF: 0.524 AC: 2709 AN: 5166

South Asian (SAS) AF: 0.575 AC: 2770 AN: 4820

European-Finnish (FIN) AF: 0.532 AC: 5636 AN: 10600

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.490 AC: 33286 AN: 67998

Other (OTH) AF: 0.446 AC: 942 AN: 2114

Alfa AF: 0.473 Hom.: 28301

Bravo AF: 0.445

Asia WGS AF: 0.537 AC: 1869 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	1.4
DANN	Benign	0.53
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10025456; hg19: chr4-10140259;