chr8-21174637-G-A

Variant names:

• chr8-21174637-G-A
• rs11991767
• ENST00000657734.1:n.1327-114702C>T

Variant summary

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

The ENST00000657734.1(ENSG00000254092):​n.1327-114702C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 151,978 control chromosomes in the GnomAD database, including 8,515 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 0.33 (8515 hom., cov: 32)
• Consequence: ENSG00000254092 ENST00000657734.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.138
• Publications: 1 publications found

Genes affected

ENSG00000254092 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000657734.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000254092	ENST00000657734.1		n.1327-114702C>T		intron	N/A
	ENSG00000254092	ENST00000659453.1		n.1640-114702C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50384 AN: 151860 Hom.: 8508 Cov.: 32

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.332 AC: 50422 AN: 151978 Hom.: 8515 Cov.: 32 AF XY: 0.330 AC XY: 24548 AN XY: 74278

African (AFR) AF: 0.362 AC: 15004 AN: 41440

American (AMR) AF: 0.263 AC: 4019 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1307 AN: 3472

East Asian (EAS) AF: 0.237 AC: 1224 AN: 5166

South Asian (SAS) AF: 0.432 AC: 2075 AN: 4800

European-Finnish (FIN) AF: 0.353 AC: 3721 AN: 10544

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 22006 AN: 67950

Other (OTH) AF: 0.350 AC: 740 AN: 2112

Alfa AF: 0.327 Hom.: 26599

Bravo AF: 0.325

Asia WGS AF: 0.370 AC: 1285 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.68
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs11991767; hg19: chr8-21032148;