ENST00000818123.1:n.191+31409T>C

Variant names:

• chr6-137466706-A-G
• rs9321611
• ENST00000818123.1:n.191+31409T>C

Variant summary

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

The ENST00000818123.1(ENSG00000306409):​n.191+31409T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.345 in 151,926 control chromosomes in the GnomAD database, including 9,869 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 0.35 (9869 hom., cov: 31)
• Consequence: ENSG00000306409 ENST00000818123.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.86
• Publications: 4 publications found

Genes affected

ENSG00000306409 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000818123.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306409	ENST00000818123.1		n.191+31409T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52394 AN: 151808 Hom.: 9857 Cov.: 31

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.345 AC: 52449 AN: 151926 Hom.: 9869 Cov.: 31 AF XY: 0.344 AC XY: 25582 AN XY: 74276

African (AFR) AF: 0.500 AC: 20692 AN: 41388

American (AMR) AF: 0.386 AC: 5892 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 753 AN: 3468

East Asian (EAS) AF: 0.217 AC: 1122 AN: 5160

South Asian (SAS) AF: 0.421 AC: 2019 AN: 4800

European-Finnish (FIN) AF: 0.246 AC: 2602 AN: 10560

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.268 AC: 18185 AN: 67952

Other (OTH) AF: 0.354 AC: 748 AN: 2112

Alfa AF: 0.331 Hom.: 1945

Bravo AF: 0.358

Asia WGS AF: 0.360 AC: 1249 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.071
DANN	Benign	0.33
PhyloP100		-3.9

Splicing

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

Other links and lift over

dbSNP: rs9321611; hg19: chr6-137787843; COSMIC: COSV50691339;