rs1343418

Variant names:

• chr10-117876439-C-T
• rs1343418

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 0.358 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
• Publications: 1 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.149 AC: 6181 AN: 41490

American (AMR) AF: 0.380 AC: 5802 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1552 AN: 3470

East Asian (EAS) AF: 0.297 AC: 1532 AN: 5162

South Asian (SAS) AF: 0.395 AC: 1903 AN: 4820

European-Finnish (FIN) AF: 0.480 AC: 5072 AN: 10570

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.459 AC: 31165 AN: 67962

Other (OTH) AF: 0.394 AC: 832 AN: 2114

Alfa AF: 0.421 Hom.: 36048

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
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs1343418; hg19: chr10-119635950;