rs1536242

Variant names:

• chr6-6930777-G-A
• rs1536242

Your query was ambiguous. Multiple possible variants found:

• chr6-6930777-G-A
• chr6-6930777-G-C
• chr6-6930777-G-T

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 0.24 in 151,950 control chromosomes in the GnomAD database, including 4,645 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 0.24 (4645 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.479 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: 0.240 AC: 36446 AN: 151832 Hom.: 4637 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.240 AC: 36480 AN: 151950 Hom.: 4645 Cov.: 32 AF XY: 0.243 AC XY: 18048 AN XY: 74262

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.495

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.202

Alfa AF: 0.212 Hom.: 1915

Bravo AF: 0.252

Asia WGS AF: 0.319 AC: 1106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.027
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: rs1536242; hg19: chr6-6931010;