rs1343043

Variant names:

• chr10-52877059-G-A
• rs1343043

Your query was ambiguous. Multiple possible variants found:

• chr10-52877059-G-A
• chr10-52877059-G-T

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 0.327 in 151,946 control chromosomes in the GnomAD database, including 8,172 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 0.33 (8172 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08
• Publications: 4 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 (EAS) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49616 AN: 151828 Hom.: 8164 Cov.: 33

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.327 AC: 49658 AN: 151946 Hom.: 8172 Cov.: 33 AF XY: 0.325 AC XY: 24161 AN XY: 74272

African (AFR) AF: 0.299 AC: 12369 AN: 41412

American (AMR) AF: 0.355 AC: 5437 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1069 AN: 3470

East Asian (EAS) AF: 0.397 AC: 2050 AN: 5160

South Asian (SAS) AF: 0.310 AC: 1490 AN: 4812

European-Finnish (FIN) AF: 0.315 AC: 3320 AN: 10544

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.336 AC: 22851 AN: 67940

Other (OTH) AF: 0.336 AC: 708 AN: 2110

Alfa AF: 0.321 Hom.: 7179

Bravo AF: 0.329

Asia WGS AF: 0.332 AC: 1156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.075
DANN	Benign	0.19
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs1343043; hg19: chr10-54636819;