rs10484434

chr6-26031385-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 0.105 in 151,814 control chromosomes in the GnomAD database, including 1,084 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 0.10 (1084 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.17 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: 0.105 AC: 15880 AN: 151694 Hom.: 1085 Cov.: 29

Gnomad AFR AF: 0.0322

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.0562

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.105 AC: 15872 AN: 151814 Hom.: 1084 Cov.: 29 AF XY: 0.105 AC XY: 7777 AN XY: 74168

Gnomad4 AFR AF: 0.0320

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.231

Gnomad4 EAS AF: 0.0564

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.127

Alfa AF: 0.138 Hom.: 3142

Bravo AF: 0.0998

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	3.1
Dann	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484434; hg19: chr6-26031613;