rs10024216

Variant names:

• chr4-38762491-G-A
• rs10024216

Your query was ambiguous. Multiple possible variants found:

• chr4-38762491-G-A
• chr4-38762491-G-T

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 0.374 in 152,028 control chromosomes in the GnomAD database, including 10,994 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 0.37 (10994 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.535 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: 0.373 AC: 56733 AN: 151908 Hom.: 10967 Cov.: 32

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.374 AC: 56786 AN: 152028 Hom.: 10994 Cov.: 32 AF XY: 0.374 AC XY: 27763 AN XY: 74286

African (AFR) AF: 0.382 AC: 15817 AN: 41458

American (AMR) AF: 0.386 AC: 5894 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1709 AN: 3472

East Asian (EAS) AF: 0.552 AC: 2853 AN: 5166

South Asian (SAS) AF: 0.491 AC: 2366 AN: 4820

European-Finnish (FIN) AF: 0.337 AC: 3563 AN: 10570

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.341 AC: 23162 AN: 67942

Other (OTH) AF: 0.441 AC: 934 AN: 2116

Alfa AF: 0.362 Hom.: 6772

Bravo AF: 0.376

Asia WGS AF: 0.496 AC: 1725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.0060
DANN	Benign	0.35
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs10024216; hg19: chr4-38764112;