6-32911456-G-T

Variant names:

• chr6-32911456-G-T
• rs154986

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 0.0858 in 152,196 control chromosomes in the GnomAD database, including 602 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 0.086 (602 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700
• Publications: 21 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.125 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: 0.0857 AC: 13035 AN: 152078 Hom.: 596 Cov.: 32

Gnomad AFR AF: 0.0969

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.0497

Gnomad ASJ AF: 0.0582

Gnomad EAS AF: 0.0859

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.0764

Gnomad NFE AF: 0.0803

Gnomad OTH AF: 0.0694

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

GnomAD4 genome AF: 0.0858 AC: 13066 AN: 152196 Hom.: 602 Cov.: 32 AF XY: 0.0886 AC XY: 6594 AN XY: 74406

African (AFR) AF: 0.0971 AC: 4033 AN: 41518

American (AMR) AF: 0.0497 AC: 760 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0582 AC: 202 AN: 3468

East Asian (EAS) AF: 0.0859 AC: 445 AN: 5178

South Asian (SAS) AF: 0.134 AC: 645 AN: 4820

European-Finnish (FIN) AF: 0.113 AC: 1197 AN: 10604

Middle Eastern (MID) AF: 0.0822 AC: 24 AN: 292

European-Non Finnish (NFE) AF: 0.0803 AC: 5462 AN: 67998

Other (OTH) AF: 0.0720 AC: 152 AN: 2110

Alfa AF: 0.0807 Hom.: 1904

Bravo AF: 0.0795

Asia WGS AF: 0.130 AC: 452 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.75
PhyloP100		-0.0070

Splicing

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

Other links and lift over

dbSNP: rs154986; hg19: chr6-32879233;