chr6-13330865-T-C

Variant names:

• chr6-13330865-T-C
• rs1512411

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 0.365 in 150,802 control chromosomes in the GnomAD database, including 10,203 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 0.36 (10203 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0630
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.556 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: 0.365 AC: 54930 AN: 150688 Hom.: 10187 Cov.: 32

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.365 AC: 54986 AN: 150802 Hom.: 10203 Cov.: 32 AF XY: 0.370 AC XY: 27233 AN XY: 73696

African (AFR) AF: 0.402 AC: 16173 AN: 40270

American (AMR) AF: 0.385 AC: 5859 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1256 AN: 3472

East Asian (EAS) AF: 0.424 AC: 2188 AN: 5162

South Asian (SAS) AF: 0.573 AC: 2758 AN: 4810

European-Finnish (FIN) AF: 0.317 AC: 3356 AN: 10582

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.327 AC: 22211 AN: 67980

Other (OTH) AF: 0.360 AC: 755 AN: 2098

Alfa AF: 0.338 Hom.: 21529

Bravo AF: 0.361

Asia WGS AF: 0.496 AC: 1721 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.51
PhyloP100		-0.063

Splicing

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

Other links and lift over

dbSNP: rs1512411; hg19: chr6-13331097;