rs6569992

Variant names:

• chr6-135131014-G-A
• rs6569992

Your query was ambiguous. Multiple possible variants found:

• chr6-135131014-G-A
• chr6-135131014-G-C
• chr6-135131014-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 0.173 in 152,096 control chromosomes in the GnomAD database, including 2,447 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 0.17 (2447 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.249 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: 0.173 AC: 26336 AN: 151978 Hom.: 2452 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.173 AC: 26334 AN: 152096 Hom.: 2447 Cov.: 32 AF XY: 0.174 AC XY: 12961 AN XY: 74346

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.261

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.256

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.159

Alfa AF: 0.187 Hom.: 4239

Bravo AF: 0.167

Asia WGS AF: 0.181 AC: 628 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.42
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6569992; hg19: chr6-135452152; COSMIC: COSV58836614;