rs10946384

Variant names:

• chr6-20495315-C-T
• rs10946384

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 0.158 in 151,848 control chromosomes in the GnomAD database, including 2,214 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 0.16 (2214 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.495
• Publications: 6 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 (SAS) allele frequency at 95% confidence interval = 0.313 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: 0.158 AC: 23980 AN: 151728 Hom.: 2215 Cov.: 31

Gnomad AFR AF: 0.0716

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.158 AC: 23977 AN: 151848 Hom.: 2214 Cov.: 31 AF XY: 0.161 AC XY: 11953 AN XY: 74228

African (AFR) AF: 0.0716 AC: 2961 AN: 41366

American (AMR) AF: 0.156 AC: 2381 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 818 AN: 3466

East Asian (EAS) AF: 0.213 AC: 1099 AN: 5150

South Asian (SAS) AF: 0.326 AC: 1564 AN: 4798

European-Finnish (FIN) AF: 0.150 AC: 1584 AN: 10570

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12907 AN: 67942

Other (OTH) AF: 0.187 AC: 395 AN: 2108

Alfa AF: 0.185 Hom.: 11454

Bravo AF: 0.152

Asia WGS AF: 0.278 AC: 968 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.1
DANN	Benign	0.49
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs10946384; hg19: chr6-20495546;