rs13201744

Variant names:

• chr6-6126612-C-A
• rs13201744

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0838 in 152,198 control chromosomes in the GnomAD database, including 635 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 0.084 (635 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.112 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: 0.0839 AC: 12753 AN: 152080 Hom.: 636 Cov.: 32

Gnomad AFR AF: 0.0477

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.0767

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.0848

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.0648

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.0860

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

GnomAD4 genome AF: 0.0838 AC: 12752 AN: 152198 Hom.: 635 Cov.: 32 AF XY: 0.0826 AC XY: 6145 AN XY: 74438

Gnomad4 AFR AF: 0.0476

Gnomad4 AMR AF: 0.0766

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.0850

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.0648

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.0870

Alfa AF: 0.0983 Hom.: 384

Bravo AF: 0.0819

Asia WGS AF: 0.0960 AC: 332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.54
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13201744; hg19: chr6-6126845;