chr6-132570037-G-A

Variant names:

• chr6-132570037-G-A
• rs17061446

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0726 in 152,050 control chromosomes in the GnomAD database, including 426 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 0.073 (426 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.803
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0786 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0726 AC: 11030 AN: 151932 Hom.: 425 Cov.: 32

Gnomad AFR AF: 0.0708

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.0819

Gnomad ASJ AF: 0.0406

Gnomad EAS AF: 0.0303

Gnomad SAS AF: 0.0182

Gnomad FIN AF: 0.0677

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0804

Gnomad OTH AF: 0.0789

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

GnomAD4 genome AF: 0.0726 AC: 11040 AN: 152050 Hom.: 426 Cov.: 32 AF XY: 0.0707 AC XY: 5252 AN XY: 74298

African (AFR) AF: 0.0709 AC: 2939 AN: 41474

American (AMR) AF: 0.0817 AC: 1249 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0406 AC: 141 AN: 3470

East Asian (EAS) AF: 0.0304 AC: 157 AN: 5172

South Asian (SAS) AF: 0.0185 AC: 89 AN: 4818

European-Finnish (FIN) AF: 0.0677 AC: 715 AN: 10556

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0804 AC: 5466 AN: 67964

Other (OTH) AF: 0.0771 AC: 163 AN: 2114

Alfa AF: 0.0747 Hom.: 152

Bravo AF: 0.0767

Asia WGS AF: 0.0280 AC: 96 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.9
DANN	Benign	0.55
PhyloP100		-0.80
PromoterAI		0.00060	Neutral

Splicing

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

Other links and lift over

dbSNP: rs17061446; hg19: chr6-132891176;