rs10001415

Variant names:

• chr4-28736466-T-C
• rs10001415

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 0.161 in 152,112 control chromosomes in the GnomAD database, including 2,832 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 0.16 (2832 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.485
• Publications: 1 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 (AFR) allele frequency at 95% confidence interval = 0.32 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: 0.161 AC: 24398 AN: 151996 Hom.: 2817 Cov.: 32

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.0150

Gnomad SAS AF: 0.0707

Gnomad FIN AF: 0.0413

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.161 AC: 24446 AN: 152112 Hom.: 2832 Cov.: 32 AF XY: 0.155 AC XY: 11513 AN XY: 74374

African (AFR) AF: 0.324 AC: 13445 AN: 41434

American (AMR) AF: 0.111 AC: 1694 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 470 AN: 3468

East Asian (EAS) AF: 0.0153 AC: 79 AN: 5172

South Asian (SAS) AF: 0.0712 AC: 344 AN: 4832

European-Finnish (FIN) AF: 0.0413 AC: 438 AN: 10612

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7486 AN: 67998

Other (OTH) AF: 0.155 AC: 328 AN: 2112

Alfa AF: 0.125 Hom.: 2409

Bravo AF: 0.176

Asia WGS AF: 0.0570 AC: 202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.76
DANN	Benign	0.33
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs10001415; hg19: chr4-28738088;