rs2564978

Variant names:

• chr1-207321071-T-C
• rs2564978
• ENST00000740658.1:n.116+615A>G

Variant summary

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

The ENST00000740658.1(ENSG00000296591):​n.116+615A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.765 in 152,128 control chromosomes in the GnomAD database, including 45,855 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 0.76 (45855 hom., cov: 32)
• Consequence: ENSG00000296591 ENST00000740658.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0300
• Publications: 40 publications found

Genes affected

ENSG00000296591 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.928 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985251	XR_007066837.1	n.444+615A>G		intron_variant	Intron 1 of 3
LOC107985251	XR_007066838.1	n.444+615A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296591	ENST00000740658.1	n.116+615A>G		intron_variant	Intron 1 of 2
ENSG00000296591	ENST00000740659.1	n.96+615A>G		intron_variant	Intron 1 of 4
ENSG00000296591	ENST00000740660.1	n.89+615A>G		intron_variant	Intron 1 of 3
ENSG00000296591	ENST00000740661.1	n.86+615A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.765 AC: 116259 AN: 152012 Hom.: 45801 Cov.: 32

Gnomad AFR AF: 0.936

Gnomad AMI AF: 0.814

Gnomad AMR AF: 0.721

Gnomad ASJ AF: 0.869

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.781

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

GnomAD4 genome AF: 0.765 AC: 116376 AN: 152128 Hom.: 45855 Cov.: 32 AF XY: 0.759 AC XY: 56440 AN XY: 74350

African (AFR) AF: 0.936 AC: 38870 AN: 41534

American (AMR) AF: 0.721 AC: 11016 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.869 AC: 3018 AN: 3472

East Asian (EAS) AF: 0.424 AC: 2178 AN: 5140

South Asian (SAS) AF: 0.579 AC: 2794 AN: 4828

European-Finnish (FIN) AF: 0.752 AC: 7948 AN: 10568

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.705 AC: 47922 AN: 67982

Other (OTH) AF: 0.777 AC: 1639 AN: 2110

Alfa AF: 0.775 Hom.: 21398

Bravo AF: 0.772

Asia WGS AF: 0.502 AC: 1751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.3
DANN	Benign	0.65
PhyloP100		-0.030
PromoterAI		0.24	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2564978; hg19: chr1-207494416;