rs1414609

Positions:

• chr10-35806516-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 0.146 in 152,068 control chromosomes in the GnomAD database, including 2,915 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 0.15 (2915 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.650

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 (AFR) allele frequency at 95% confidence interval = 0.346 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: 0.146 AC: 22151 AN: 151952 Hom.: 2898 Cov.: 32

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0792

Gnomad ASJ AF: 0.0481

Gnomad EAS AF: 0.00327

Gnomad SAS AF: 0.0874

Gnomad FIN AF: 0.0525

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0731

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.146 AC: 22213 AN: 152068 Hom.: 2915 Cov.: 32 AF XY: 0.142 AC XY: 10582 AN XY: 74360

Gnomad4 AFR AF: 0.351

Gnomad4 AMR AF: 0.0791

Gnomad4 ASJ AF: 0.0481

Gnomad4 EAS AF: 0.00347

Gnomad4 SAS AF: 0.0877

Gnomad4 FIN AF: 0.0525

Gnomad4 NFE AF: 0.0731

Gnomad4 OTH AF: 0.127

Alfa AF: 0.115 Hom.: 301

Bravo AF: 0.155

Asia WGS AF: 0.0770 AC: 269 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	0.71
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1414609; hg19: chr10-36095444;