rs2927071

Variant names:

• chr15-43626883-T-C
• rs2927071
• ENST00000643290.1:n.85+5316A>G

Variant summary

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

The ENST00000643290.1(ENSG00000284772):​n.85+5316A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 151,702 control chromosomes in the GnomAD database, including 13,623 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 0.38 (13623 hom., cov: 32)
• Consequence: ENSG00000284772 ENST00000643290.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.492
• Publications: 22 publications found

Genes affected

ENSG00000284772 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000284772	ENST00000643290.1	n.85+5316A>G		intron_variant	Intron 1 of 8			ENSP00000495476.1
ENSG00000309475	ENST00000841330.1	n.364-1002T>C		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57424 AN: 151584 Hom.: 13579 Cov.: 32

Gnomad AFR AF: 0.653

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.379 AC: 57520 AN: 151702 Hom.: 13623 Cov.: 32 AF XY: 0.372 AC XY: 27596 AN XY: 74132

African (AFR) AF: 0.654 AC: 27015 AN: 41306

American (AMR) AF: 0.339 AC: 5169 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1296 AN: 3464

East Asian (EAS) AF: 0.279 AC: 1436 AN: 5154

South Asian (SAS) AF: 0.349 AC: 1676 AN: 4804

European-Finnish (FIN) AF: 0.144 AC: 1523 AN: 10560

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18319 AN: 67866

Other (OTH) AF: 0.362 AC: 757 AN: 2092

Alfa AF: 0.315 Hom.: 12227

Bravo AF: 0.406

Asia WGS AF: 0.324 AC: 1129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.29
PhyloP100		-0.49
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2927071; hg19: chr15-43919081;