rs1414609

Variant names:

• chr10-35806516-G-A
• rs1414609

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.351 AC: 14532 AN: 41410

American (AMR) AF: 0.0791 AC: 1208 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0481 AC: 167 AN: 3470

East Asian (EAS) AF: 0.00347 AC: 18 AN: 5186

South Asian (SAS) AF: 0.0877 AC: 422 AN: 4812

European-Finnish (FIN) AF: 0.0525 AC: 556 AN: 10592

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0731 AC: 4970 AN: 68000

Other (OTH) AF: 0.127 AC: 268 AN: 2112

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
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs1414609; hg19: chr10-36095444;