rs10807439

Variant names:

• chr6-52233314-C-T
• rs10807439

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 0.412 in 151,998 control chromosomes in the GnomAD database, including 13,700 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 0.41 (13700 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.139
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.488 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: 0.412 AC: 62646 AN: 151878 Hom.: 13697 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.412 AC: 62668 AN: 151998 Hom.: 13700 Cov.: 32 AF XY: 0.417 AC XY: 30945 AN XY: 74294

African (AFR) AF: 0.267 AC: 11062 AN: 41470

American (AMR) AF: 0.352 AC: 5380 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1526 AN: 3466

East Asian (EAS) AF: 0.504 AC: 2609 AN: 5178

South Asian (SAS) AF: 0.491 AC: 2361 AN: 4812

European-Finnish (FIN) AF: 0.553 AC: 5839 AN: 10556

Middle Eastern (MID) AF: 0.476 AC: 139 AN: 292

European-Non Finnish (NFE) AF: 0.478 AC: 32478 AN: 67926

Other (OTH) AF: 0.426 AC: 897 AN: 2108

Alfa AF: 0.409 Hom.: 2011

Bravo AF: 0.389

Asia WGS AF: 0.434 AC: 1507 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.68
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs10807439; hg19: chr6-52098112;