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).

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: 0.00161 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 = 0.000000), 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 v4.3

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

Other links and lift over

dbSNP: rs9271871; hg19: chr6-32595383;