rs169713

chr6-11920284-T-C

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 152,042 control chromosomes in the GnomAD database, including 9,289 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 (9289 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0340

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 (AFR) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47083 AN: 151926 Hom.: 9256 Cov.: 32

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.0516

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.310 AC: 47159 AN: 152042 Hom.: 9289 Cov.: 32 AF XY: 0.306 AC XY: 22769 AN XY: 74344

Gnomad4 AFR AF: 0.559

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.199

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.338

Alfa AF: 0.242 Hom.: 6728

Bravo AF: 0.320

Asia WGS AF: 0.253 AC: 885 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	0.67
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs169713; hg19: chr6-11920517;