rs10517437

chr4-58142246-G-Achr4-58142246-G-C

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 0.445 in 151,390 control chromosomes in the GnomAD database, including 15,618 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 0.44 (15618 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.269

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.445 AC: 67335 AN: 151272 Hom.: 15615 Cov.: 31

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.445 AC: 67358 AN: 151390 Hom.: 15618 Cov.: 31 AF XY: 0.449 AC XY: 33183 AN XY: 73966

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.592

Gnomad4 EAS AF: 0.379

Gnomad4 SAS AF: 0.616

Gnomad4 FIN AF: 0.488

Gnomad4 NFE AF: 0.504

Gnomad4 OTH AF: 0.474

Alfa AF: 0.494 Hom.: 38481

Bravo AF: 0.432

Asia WGS AF: 0.467 AC: 1618 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	4.5
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517437; hg19: chr4-59008412;