6-32690302-T-C

Variant names:

• chr6-32690302-T-C
• rs7775228
• ENST00000790899.1:n.53A>G

Variant summary

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

The ENST00000790899.1(ENSG00000302994):​n.53A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 151,460 control chromosomes in the GnomAD database, including 2,037 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 0.16 (2037 hom., cov: 31)
• Consequence: ENSG00000302994 ENST00000790899.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 128 publications found

Genes affected

ENSG00000302994 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000790899.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000302994	ENST00000790899.1		n.53A>G		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23664 AN: 151342 Hom.: 2038 Cov.: 31

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.0868

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.156 AC: 23678 AN: 151460 Hom.: 2037 Cov.: 31 AF XY: 0.160 AC XY: 11849 AN XY: 73994

African (AFR) AF: 0.169 AC: 6976 AN: 41256

American (AMR) AF: 0.189 AC: 2883 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 587 AN: 3464

East Asian (EAS) AF: 0.250 AC: 1279 AN: 5122

South Asian (SAS) AF: 0.270 AC: 1276 AN: 4734

European-Finnish (FIN) AF: 0.152 AC: 1599 AN: 10548

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8589 AN: 67812

Other (OTH) AF: 0.174 AC: 364 AN: 2096

Alfa AF: 0.139 Hom.: 6026

Bravo AF: 0.163

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.9
DANN	Benign	0.59
PhyloP100		-1.1

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: rs7775228;

hg19: chr6-32658079;