rs2853934

Variant names:

• chr6-31286151-A-T
• rs2853934
• ENST00000755297.1:n.32+15045A>T

Variant summary

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

The ENST00000755297.1(ENSG00000298396):​n.32+15045A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,284 control chromosomes in the GnomAD database, including 907 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 0.10 (907 hom., cov: 33)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.636
• Publications: 14 publications found

Genes affected

ENSG00000298396 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.122 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
ENSG00000298396	ENST00000755297.1	n.32+15045A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15702 AN: 152166 Hom.: 908 Cov.: 33

Gnomad AFR AF: 0.0763

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.0713

Gnomad FIN AF: 0.0526

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.103 AC: 15699 AN: 152284 Hom.: 907 Cov.: 33 AF XY: 0.0977 AC XY: 7278 AN XY: 74458

African (AFR) AF: 0.0762 AC: 3165 AN: 41540

American (AMR) AF: 0.115 AC: 1755 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 522 AN: 3470

East Asian (EAS) AF: 0.103 AC: 535 AN: 5188

South Asian (SAS) AF: 0.0710 AC: 343 AN: 4834

European-Finnish (FIN) AF: 0.0526 AC: 558 AN: 10614

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8449 AN: 68016

Other (OTH) AF: 0.114 AC: 242 AN: 2116

Alfa AF: 0.105 Hom.: 119

Bravo AF: 0.108

Asia WGS AF: 0.0870 AC: 303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.8
DANN	Benign	0.69
PhyloP100		0.64

Splicing

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

Other links and lift over

dbSNP: rs2853934; hg19: chr6-31253928;