rs10043360

Variant names:

• chr5-136064368-T-A
• rs10043360

Your query was ambiguous. Multiple possible variants found:

• chr5-136064368-T-A
• chr5-136064368-T-C

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 0.183 in 152,058 control chromosomes in the GnomAD database, including 2,608 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 0.18 (2608 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.465
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.217 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: 0.183 AC: 27753 AN: 151940 Hom.: 2603 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.0660

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.183 AC: 27766 AN: 152058 Hom.: 2608 Cov.: 32 AF XY: 0.180 AC XY: 13402 AN XY: 74322

African (AFR) AF: 0.176 AC: 7314 AN: 41462

American (AMR) AF: 0.223 AC: 3412 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 585 AN: 3470

East Asian (EAS) AF: 0.120 AC: 621 AN: 5162

South Asian (SAS) AF: 0.0657 AC: 316 AN: 4812

European-Finnish (FIN) AF: 0.191 AC: 2021 AN: 10578

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12916 AN: 67978

Other (OTH) AF: 0.201 AC: 425 AN: 2112

Alfa AF: 0.102 Hom.: 143

Bravo AF: 0.192

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.91
DANN	Benign	0.55
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs10043360; hg19: chr5-135400057;