4-60288620-T-C

Variant names:

• chr4-60288620-T-C
• rs10517502

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 0.697 in 152,012 control chromosomes in the GnomAD database, including 38,985 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 0.70 (38985 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.493

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.82 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: 0.697 AC: 105904 AN: 151896 Hom.: 38988 Cov.: 31

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.784

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.794

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.826

Gnomad OTH AF: 0.725

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

GnomAD4 genome AF: 0.697 AC: 105920 AN: 152012 Hom.: 38985 Cov.: 31 AF XY: 0.693 AC XY: 51495 AN XY: 74282

Gnomad4 AFR AF: 0.459

Gnomad4 AMR AF: 0.767

Gnomad4 ASJ AF: 0.789

Gnomad4 EAS AF: 0.498

Gnomad4 SAS AF: 0.599

Gnomad4 FIN AF: 0.794

Gnomad4 NFE AF: 0.826

Gnomad4 OTH AF: 0.717

Alfa AF: 0.801 Hom.: 49026

Bravo AF: 0.688

Asia WGS AF: 0.508 AC: 1767 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.5
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517502; hg19: chr4-61154338;