rs511027

Variant names:

• chr6-32238910-A-T
• rs511027

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 0.111 in 152,120 control chromosomes in the GnomAD database, including 1,090 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 0.11 (1090 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.559
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.146 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: 0.111 AC: 16801 AN: 152002 Hom.: 1090 Cov.: 31

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.0845

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.0653

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.111 AC: 16816 AN: 152120 Hom.: 1090 Cov.: 31 AF XY: 0.109 AC XY: 8119 AN XY: 74394

African (AFR) AF: 0.103 AC: 4257 AN: 41496

American (AMR) AF: 0.151 AC: 2309 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 496 AN: 3470

East Asian (EAS) AF: 0.0847 AC: 439 AN: 5184

South Asian (SAS) AF: 0.144 AC: 695 AN: 4822

European-Finnish (FIN) AF: 0.0653 AC: 691 AN: 10588

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7539 AN: 67980

Other (OTH) AF: 0.124 AC: 262 AN: 2112

Alfa AF: 0.0990 Hom.: 126

Bravo AF: 0.118

Asia WGS AF: 0.100 AC: 347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.1
DANN	Benign	0.49
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs511027; hg19: chr6-32206687;