ENST00000615176.1:n.977-7361A>C

Variant names:

• chr13-53402639-A-C
• rs2165985
• ENST00000615176.1:n.977-7361A>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000615176.1(ENSG00000273919):​n.977-7361A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 151,998 control chromosomes in the GnomAD database, including 14,749 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 0.44 (14749 hom., cov: 33)
• Consequence: ENSG00000273919 ENST00000615176.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.172
• Publications: 2 publications found

Genes affected

ENSG00000273919 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000615176.1. 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
	ENSG00000273919	ENST00000615176.1	TSL:2	n.977-7361A>C		intron	N/A
	ENSG00000287722	ENST00000657016.1		n.629+98517A>C		intron	N/A
	ENSG00000288768	ENST00000688155.1		n.46-20141A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66083 AN: 151878 Hom.: 14741 Cov.: 33

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.435 AC: 66126 AN: 151998 Hom.: 14749 Cov.: 33 AF XY: 0.438 AC XY: 32571 AN XY: 74280

African (AFR) AF: 0.367 AC: 15212 AN: 41468

American (AMR) AF: 0.524 AC: 7999 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1592 AN: 3472

East Asian (EAS) AF: 0.450 AC: 2322 AN: 5160

South Asian (SAS) AF: 0.474 AC: 2286 AN: 4826

European-Finnish (FIN) AF: 0.445 AC: 4688 AN: 10534

Middle Eastern (MID) AF: 0.476 AC: 139 AN: 292

European-Non Finnish (NFE) AF: 0.448 AC: 30418 AN: 67952

Other (OTH) AF: 0.457 AC: 964 AN: 2110

Alfa AF: 0.378 Hom.: 1999

Bravo AF: 0.439

Asia WGS AF: 0.456 AC: 1581 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	17
DANN	Benign	0.78
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs2165985; hg19: chr13-53976774;