chr6-13553811-A-G

Position:

• chr6-13553811-A-G

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 0.31 in 152,196 control chromosomes in the GnomAD database, including 7,697 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 0.31 (7697 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.791

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47165 AN: 152078 Hom.: 7684 Cov.: 33

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.310 AC: 47214 AN: 152196 Hom.: 7697 Cov.: 33 AF XY: 0.308 AC XY: 22915 AN XY: 74418

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.384

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.230

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.354

Gnomad4 OTH AF: 0.342

Alfa AF: 0.351 Hom.: 14229

Bravo AF: 0.310

Asia WGS AF: 0.263 AC: 919 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.7
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4712032; hg19: chr6-13554043;