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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900354	XR_001751516.3	n.143-20411T>G		intron_variant	Intron 1 of 2
LOC124900354	XR_001751517.2	n.143-20411T>G		intron_variant	Intron 1 of 2
LOC124900354	XR_001751518.3	n.83-20411T>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259754	ENST00000560900.1	n.196-20411T>G		intron_variant	Intron 1 of 2	4
ENSG00000287439	ENST00000657831.2	n.442-11673A>C		intron_variant	Intron 1 of 2
ENSG00000259754	ENST00000662551.1	n.189-20411T>G		intron_variant	Intron 1 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs2965318; hg19: chr15-48264495;