rs10940434

Positions:

• chr5-54879078-T-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 0.493 in 151,928 control chromosomes in the GnomAD database, including 21,069 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 (21069 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.333

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.493 AC: 74863 AN: 151810 Hom.: 21063 Cov.: 31

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.551

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.493 AC: 74880 AN: 151928 Hom.: 21069 Cov.: 31 AF XY: 0.498 AC XY: 36992 AN XY: 74260

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.624

Gnomad4 ASJ AF: 0.477

Gnomad4 EAS AF: 0.616

Gnomad4 SAS AF: 0.474

Gnomad4 FIN AF: 0.643

Gnomad4 NFE AF: 0.603

Gnomad4 OTH AF: 0.495

Alfa AF: 0.578 Hom.: 43676

Bravo AF: 0.483

Asia WGS AF: 0.496 AC: 1722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.46
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10940434; hg19: chr5-54174906;