rs1343418

Positions:

• chr10-117876439-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 0.358 in 152,070 control chromosomes in the GnomAD database, including 11,117 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 0.36 (11117 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.710

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.454 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: 0.359 AC: 54489 AN: 151952 Hom.: 11123 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.358 AC: 54497 AN: 152070 Hom.: 11117 Cov.: 32 AF XY: 0.361 AC XY: 26805 AN XY: 74342

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.380

Gnomad4 ASJ AF: 0.447

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.480

Gnomad4 NFE AF: 0.459

Gnomad4 OTH AF: 0.394

Alfa AF: 0.440 Hom.: 13728

Bravo AF: 0.343

Asia WGS AF: 0.325 AC: 1130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.91
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1343418; hg19: chr10-119635950;