rs2965318

Variant names:

• chr15-47972298-T-G
• rs2965318
• ENST00000560900.1:n.196-20411T>G

Variant summary

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

The ENST00000560900.1(ENSG00000259754):​n.196-20411T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.849 in 151,622 control chromosomes in the GnomAD database, including 56,335 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 0.85 (56335 hom., cov: 31)
• Consequence: ENSG00000259754 ENST00000560900.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.34
• Publications: 2 publications found

Genes affected

ENSG00000259754 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000560900.1. 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
	ENSG00000259754	ENST00000560900.1	TSL:4	n.196-20411T>G		intron	N/A
	ENSG00000287439	ENST00000657831.2		n.442-11673A>C		intron	N/A
	ENSG00000259754	ENST00000662551.1		n.189-20411T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.850 AC: 128737 AN: 151506 Hom.: 56328 Cov.: 31

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.952

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.953

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.942

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.961

Gnomad OTH AF: 0.873

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

GnomAD4 genome AF: 0.849 AC: 128786 AN: 151622 Hom.: 56335 Cov.: 31 AF XY: 0.847 AC XY: 62752 AN XY: 74116

African (AFR) AF: 0.671 AC: 27507 AN: 40984

American (AMR) AF: 0.827 AC: 12625 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.953 AC: 3304 AN: 3468

East Asian (EAS) AF: 0.614 AC: 3156 AN: 5140

South Asian (SAS) AF: 0.793 AC: 3816 AN: 4812

European-Finnish (FIN) AF: 0.942 AC: 9993 AN: 10608

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.961 AC: 65400 AN: 68022

Other (OTH) AF: 0.872 AC: 1840 AN: 2110

Alfa AF: 0.917 Hom.: 191004

Bravo AF: 0.831

Asia WGS AF: 0.697 AC: 2422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.073
DANN	Benign	0.71
PhyloP100		-2.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2965318;

hg19: chr15-48264495;