rs10488929

Positions:

• chr4-81411321-C-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 0.0419 in 152,210 control chromosomes in the GnomAD database, including 330 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 0.042 (330 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.103

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.115 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: 0.0418 AC: 6361 AN: 152092 Hom.: 331 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0214

Gnomad ASJ AF: 0.0438

Gnomad EAS AF: 0.0108

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.000848

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.00478

Gnomad OTH AF: 0.0460

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

GnomAD4 genome AF: 0.0419 AC: 6371 AN: 152210 Hom.: 330 Cov.: 32 AF XY: 0.0423 AC XY: 3146 AN XY: 74422

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.0214

Gnomad4 ASJ AF: 0.0438

Gnomad4 EAS AF: 0.0108

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.000848

Gnomad4 NFE AF: 0.00478

Gnomad4 OTH AF: 0.0464

Alfa AF: 0.0131 Hom.: 42

Bravo AF: 0.0445

Asia WGS AF: 0.0790 AC: 277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.6
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10488929; hg19: chr4-82332475;