chr4-25637114-T-G

Variant names:

• chr4-25637114-T-G
• rs10517077

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 0.306 in 152,144 control chromosomes in the GnomAD database, including 9,622 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 0.31 (9622 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.57 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: 0.306 AC: 46468 AN: 152026 Hom.: 9578 Cov.: 32

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.306 AC: 46576 AN: 152144 Hom.: 9622 Cov.: 32 AF XY: 0.307 AC XY: 22845 AN XY: 74384

African (AFR) AF: 0.576 AC: 23898 AN: 41492

American (AMR) AF: 0.310 AC: 4734 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 576 AN: 3470

East Asian (EAS) AF: 0.385 AC: 1989 AN: 5170

South Asian (SAS) AF: 0.274 AC: 1320 AN: 4824

European-Finnish (FIN) AF: 0.149 AC: 1579 AN: 10602

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11562 AN: 68004

Other (OTH) AF: 0.300 AC: 632 AN: 2108

Alfa AF: 0.209 Hom.: 16697

Bravo AF: 0.331

Asia WGS AF: 0.333 AC: 1157 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.6
DANN	Benign	0.60
PhyloP100		-0.0020

Splicing

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

Other links and lift over

dbSNP: rs10517077; hg19: chr4-25638736;