rs10041997

Positions:

• chr5-120862616-G-A

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 0.485 in 151,820 control chromosomes in the GnomAD database, including 17,907 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 0.49 (17907 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.22

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.554 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: 0.485 AC: 73586 AN: 151698 Hom.: 17854 Cov.: 32

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.485 AC: 73703 AN: 151820 Hom.: 17907 Cov.: 32 AF XY: 0.491 AC XY: 36433 AN XY: 74192

Gnomad4 AFR AF: 0.510

Gnomad4 AMR AF: 0.535

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.544

Gnomad4 SAS AF: 0.571

Gnomad4 FIN AF: 0.486

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.477

Alfa AF: 0.457 Hom.: 31308

Bravo AF: 0.488

Asia WGS AF: 0.572 AC: 1986 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.023
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10041997; hg19: chr5-120198311;