rs853361

Variant names:

• chr6-14137907-C-T
• rs853361

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 0.746 in 152,178 control chromosomes in the GnomAD database, including 42,890 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 0.75 (42890 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.799 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: 0.746 AC: 113411 AN: 152060 Hom.: 42844 Cov.: 33

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.744

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.805

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.746 AC: 113518 AN: 152178 Hom.: 42890 Cov.: 33 AF XY: 0.737 AC XY: 54852 AN XY: 74394

Gnomad4 AFR AF: 0.721

Gnomad4 AMR AF: 0.732

Gnomad4 ASJ AF: 0.752

Gnomad4 EAS AF: 0.356

Gnomad4 SAS AF: 0.584

Gnomad4 FIN AF: 0.744

Gnomad4 NFE AF: 0.805

Gnomad4 OTH AF: 0.729

Alfa AF: 0.783 Hom.: 10610

Bravo AF: 0.744

Asia WGS AF: 0.491 AC: 1708 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.17
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs853361; hg19: chr6-14138138;