rs10452621

Variant names:

• chr6-131764261-C-T
• rs10452621

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 0.142 in 152,168 control chromosomes in the GnomAD database, including 2,097 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 0.14 (2097 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.190
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.437 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: 0.142 AC: 21630 AN: 152050 Hom.: 2091 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.0866

Gnomad MID AF: 0.0605

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.142 AC: 21667 AN: 152168 Hom.: 2097 Cov.: 32 AF XY: 0.146 AC XY: 10873 AN XY: 74392

African (AFR) AF: 0.129 AC: 5354 AN: 41526

American (AMR) AF: 0.256 AC: 3912 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 364 AN: 3466

East Asian (EAS) AF: 0.452 AC: 2330 AN: 5154

South Asian (SAS) AF: 0.199 AC: 958 AN: 4824

European-Finnish (FIN) AF: 0.0866 AC: 917 AN: 10586

Middle Eastern (MID) AF: 0.0616 AC: 18 AN: 292

European-Non Finnish (NFE) AF: 0.107 AC: 7307 AN: 68010

Other (OTH) AF: 0.136 AC: 288 AN: 2116

Alfa AF: 0.121 Hom.: 629

Bravo AF: 0.155

Asia WGS AF: 0.298 AC: 1032 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.25
DANN	Benign	0.61
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs10452621; hg19: chr6-132085401;