rs921298

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000663591.1(ENSG00000287092):​n.398+157465G>T variant causes a intron, non coding transcript 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: ENST00000663591.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0440

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928923	XR_001744423.2	n.405+73481G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000663591.1	n.398+157465G>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.385

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.420

Gnomad4 EAS AF: 0.482

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.423

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.382

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs921298; hg19: chr6-156415989;