chr6-32446496-T-C

Variant names:

• chr6-32446496-T-C
• rs3129890
• ENST00000766007.1:n.163-8236A>G

Variant summary

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

The ENST00000766007.1(ENSG00000299747):​n.163-8236A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 149,974 control chromosomes in the GnomAD database, including 6,645 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 0.29 (6645 hom., cov: 28)
• Consequence: ENSG00000299747 ENST00000766007.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.547
• Publications: 81 publications found

Genes affected

ENSG00000299747 (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 (AFR) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000766007.1. 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
	ENSG00000299747	ENST00000766007.1		n.163-8236A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.292 AC: 43787 AN: 149888 Hom.: 6631 Cov.: 28

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.292 AC: 43838 AN: 149974 Hom.: 6645 Cov.: 28 AF XY: 0.292 AC XY: 21330 AN XY: 73070

African (AFR) AF: 0.357 AC: 14564 AN: 40748

American (AMR) AF: 0.260 AC: 3905 AN: 15030

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 760 AN: 3462

East Asian (EAS) AF: 0.311 AC: 1581 AN: 5082

South Asian (SAS) AF: 0.252 AC: 1203 AN: 4782

European-Finnish (FIN) AF: 0.341 AC: 3346 AN: 9820

Middle Eastern (MID) AF: 0.231 AC: 67 AN: 290

European-Non Finnish (NFE) AF: 0.261 AC: 17688 AN: 67760

Other (OTH) AF: 0.291 AC: 608 AN: 2088

Alfa AF: 0.276 Hom.: 22961

Bravo AF: 0.291

Asia WGS AF: 0.325 AC: 1129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.0
DANN	Benign	0.55
PhyloP100		-0.55

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: rs3129890;

hg19: chr6-32414273;