6-32627606-T-C

Variant names:

• chr6-32627606-T-C
• rs9271871

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

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 0.0016 (0 hom., cov: 16)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53
• Publications: 6 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).

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: 0.00161 AC: 159 AN: 98810 Hom.: 0 Cov.: 16

Gnomad AFR AF: 0.00179

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00237

Gnomad ASJ AF: 0.000977

Gnomad EAS AF: 0.000486

Gnomad SAS AF: 0.00136

Gnomad FIN AF: 0.00173

Gnomad MID AF: 0.0116

Gnomad NFE AF: 0.00145

Gnomad OTH AF: 0.00163

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

GnomAD4 genome AF: 0.00160 AC: 158 AN: 98870 Hom.: 0 Cov.: 16 AF XY: 0.00158 AC XY: 76 AN XY: 48068

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00174 AC: 47 AN: 26938

American (AMR) AF: 0.00237 AC: 23 AN: 9722

Ashkenazi Jewish (ASJ) AF: 0.000977 AC: 2 AN: 2048

East Asian (EAS) AF: 0.000486 AC: 2 AN: 4114

South Asian (SAS) AF: 0.00137 AC: 4 AN: 2928

European-Finnish (FIN) AF: 0.00173 AC: 11 AN: 6374

Middle Eastern (MID) AF: 0.0128 AC: 2 AN: 156

European-Non Finnish (NFE) AF: 0.00145 AC: 65 AN: 44712

Other (OTH) AF: 0.00160 AC: 2 AN: 1248

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.0201 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.7
DANN	Benign	0.11
PhyloP100		-1.5

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9271871;

hg19: chr6-32595383;