chr4-60288620-T-C

Variant names:

• chr4-60288620-T-C
• rs10517502

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 0.697 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
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.82 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: 0.697 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

African (AFR) AF: 0.459 AC: 19004 AN: 41434

American (AMR) AF: 0.767 AC: 11699 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.789 AC: 2740 AN: 3472

East Asian (EAS) AF: 0.498 AC: 2567 AN: 5150

South Asian (SAS) AF: 0.599 AC: 2884 AN: 4818

European-Finnish (FIN) AF: 0.794 AC: 8383 AN: 10554

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.826 AC: 56166 AN: 68006

Other (OTH) AF: 0.717 AC: 1513 AN: 2110

Alfa AF: 0.786 Hom.: 61854

Bravo AF: 0.688

Asia WGS AF: 0.508 AC: 1767 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.5
DANN	Benign	0.51
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs10517502; hg19: chr4-61154338;