rs2927071

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000284772 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.654

Gnomad4 AMR AF: 0.339

Gnomad4 ASJ AF: 0.374

Gnomad4 EAS AF: 0.279

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.362

Alfa AF: 0.302 Hom.: 8264

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2927071; hg19: chr15-43919081;