rs10040610

Variant names:

• chr5-6353702-T-C
• rs10040610

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 0.151 in 152,176 control chromosomes in the GnomAD database, including 2,021 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 (2021 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0440
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22971 AN: 152058 Hom.: 2018 Cov.: 33

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.0899

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.151 AC: 22999 AN: 152176 Hom.: 2021 Cov.: 33 AF XY: 0.154 AC XY: 11492 AN XY: 74408

African (AFR) AF: 0.218 AC: 9063 AN: 41510

American (AMR) AF: 0.147 AC: 2251 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0899 AC: 312 AN: 3472

East Asian (EAS) AF: 0.319 AC: 1648 AN: 5164

South Asian (SAS) AF: 0.173 AC: 837 AN: 4832

European-Finnish (FIN) AF: 0.109 AC: 1152 AN: 10608

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7348 AN: 67978

Other (OTH) AF: 0.128 AC: 271 AN: 2112

Alfa AF: 0.124 Hom.: 5954

Bravo AF: 0.155

Asia WGS AF: 0.242 AC: 841 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.8
DANN	Benign	0.36
PhyloP100		0.044

Splicing

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

Other links and lift over

dbSNP: rs10040610; hg19: chr5-6353815;