rs2631879

Positions:

• chr8-21273191-C-T

Variant summary

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

The ENST00000659453.1(ENSG00000254092):​n.1639+21943G>A 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 0.253 in 152,070 control chromosomes in the GnomAD database, including 8,211 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 0.25 (8211 hom., cov: 32)
• Consequence: ENST00000659453.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.759

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000659453.1	n.1639+21943G>A		intron_variant, non_coding_transcript_variant
	ENST00000657734.1	n.1326+21943G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38347 AN: 151954 Hom.: 8193 Cov.: 32

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.0659

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.0740

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.253 AC: 38404 AN: 152070 Hom.: 8211 Cov.: 32 AF XY: 0.246 AC XY: 18275 AN XY: 74358

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.146

Gnomad4 EAS AF: 0.0659

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.0740

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.237

Alfa AF: 0.152 Hom.: 3563

Bravo AF: 0.279

Asia WGS AF: 0.132 AC: 463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.53
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2631879; hg19: chr8-21130702;