rs921298

Variant names:

• chr6-156094855-C-A
• rs921298
• ENST00000663591.1:n.398+157465G>T

Your query was ambiguous. Multiple possible variants found:

• chr6-156094855-C-A
• chr6-156094855-C-T

Variant summary

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

The ENST00000663591.1(ENSG00000287092):​n.398+157465G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 151,982 control chromosomes in the GnomAD database, including 10,573 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 0.37 (10573 hom., cov: 32)
• Consequence: ENSG00000287092 ENST00000663591.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0440
• Publications: 3 publications found

Genes affected

ENSG00000287092 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000663591.1. 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
	ENSG00000287092	ENST00000663591.1		n.398+157465G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56157 AN: 151864 Hom.: 10558 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.370 AC: 56192 AN: 151982 Hom.: 10573 Cov.: 32 AF XY: 0.373 AC XY: 27730 AN XY: 74298

African (AFR) AF: 0.385 AC: 15962 AN: 41444

American (AMR) AF: 0.257 AC: 3923 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1458 AN: 3470

East Asian (EAS) AF: 0.482 AC: 2487 AN: 5164

South Asian (SAS) AF: 0.451 AC: 2176 AN: 4822

European-Finnish (FIN) AF: 0.423 AC: 4455 AN: 10538

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.359 AC: 24428 AN: 67960

Other (OTH) AF: 0.382 AC: 803 AN: 2102

Alfa AF: 0.353 Hom.: 1682

Bravo AF: 0.357

Asia WGS AF: 0.475 AC: 1647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.5
DANN	Benign	0.36
PhyloP100		0.044

Splicing

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

Other links and lift over

dbSNP: rs921298; hg19: chr6-156415989;