chr6-130550413-T-C

Variant names:

• chr6-130550413-T-C
• rs1203344

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 0.535 in 151,978 control chromosomes in the GnomAD database, including 23,058 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 0.54 (23058 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.287
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.746 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: 0.535 AC: 81243 AN: 151860 Hom.: 23023 Cov.: 32

Gnomad AFR AF: 0.707

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.530

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

GnomAD4 genome AF: 0.535 AC: 81332 AN: 151978 Hom.: 23058 Cov.: 32 AF XY: 0.540 AC XY: 40092 AN XY: 74270

African (AFR) AF: 0.707 AC: 29290 AN: 41454

American (AMR) AF: 0.484 AC: 7391 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.527 AC: 1829 AN: 3470

East Asian (EAS) AF: 0.766 AC: 3950 AN: 5158

South Asian (SAS) AF: 0.644 AC: 3102 AN: 4814

European-Finnish (FIN) AF: 0.456 AC: 4819 AN: 10562

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.432 AC: 29375 AN: 67946

Other (OTH) AF: 0.535 AC: 1129 AN: 2112

Alfa AF: 0.501 Hom.: 2553

Bravo AF: 0.542

Asia WGS AF: 0.710 AC: 2468 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.2
DANN	Benign	0.52
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs1203344; hg19: chr6-130871558; COSMIC: COSV69426260;