rs2844615

Variant names:

• chr6-31275182-C-T
• rs2844615
• ENST00000755297.1:n.32+4076C>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+4076C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,242 control chromosomes in the GnomAD database, including 1,045 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 0.11 (1045 hom., cov: 33)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85
• Publications: 7 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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755297.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298396	ENST00000755297.1		n.32+4076C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17284 AN: 152122 Hom.: 1044 Cov.: 33

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.0675

Gnomad FIN AF: 0.0525

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.114 AC: 17284 AN: 152242 Hom.: 1045 Cov.: 33 AF XY: 0.108 AC XY: 8065 AN XY: 74424

African (AFR) AF: 0.112 AC: 4668 AN: 41524

American (AMR) AF: 0.119 AC: 1818 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 522 AN: 3468

East Asian (EAS) AF: 0.105 AC: 546 AN: 5182

South Asian (SAS) AF: 0.0671 AC: 324 AN: 4828

European-Finnish (FIN) AF: 0.0525 AC: 556 AN: 10596

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8467 AN: 68022

Other (OTH) AF: 0.121 AC: 255 AN: 2114

Alfa AF: 0.118 Hom.: 645

Bravo AF: 0.120

Asia WGS AF: 0.0870 AC: 305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.2
DANN	Benign	0.33
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs2844615; hg19: chr6-31242959;