rs10024216

Positions:

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

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 0.374 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.38762491G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.386

Gnomad4 ASJ AF: 0.492

Gnomad4 EAS AF: 0.552

Gnomad4 SAS AF: 0.491

Gnomad4 FIN AF: 0.337

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.441

Alfa AF: 0.363 Hom.: 6227

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10024216; hg19: chr4-38764112;