rs742206

chr6-15669067-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 0.142 in 152,146 control chromosomes in the GnomAD database, including 2,059 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 0.14 (2059 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.266 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: 0.142 AC: 21531 AN: 152028 Hom.: 2063 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.0741

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.0499

Gnomad FIN AF: 0.0702

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.0939

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.142 AC: 21538 AN: 152146 Hom.: 2059 Cov.: 32 AF XY: 0.137 AC XY: 10229 AN XY: 74398

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.0741

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.0506

Gnomad4 FIN AF: 0.0702

Gnomad4 NFE AF: 0.0939

Gnomad4 OTH AF: 0.121

Alfa AF: 0.126 Hom.: 584

Bravo AF: 0.156

Asia WGS AF: 0.0350 AC: 123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.1
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs742206; hg19: chr6-15669298;