rs742206

Variant names:

• chr6-15669067-T-C
• rs742206

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;