rs2215564

Variant names:

• chr7-150866876-T-C
• rs2215564
• ENST00000685404.2:n.1556A>G

Variant summary

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

The ENST00000685404.2(ENSG00000289052):​n.1556A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.087 in 152,272 control chromosomes in the GnomAD database, including 734 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 0.087 (734 hom., cov: 33)
• Consequence: ENSG00000289052 ENST00000685404.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700
• Publications: 6 publications found

Genes affected

ENSG00000289052 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.124 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375567	XR_928169.3	n.122+10133A>G		intron_variant	Intron 1 of 3
LOC105375567	XR_928171.3	n.122+10133A>G		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289052	ENST00000685404.2	n.1556A>G		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000289052	ENST00000726369.1	n.270+10133A>G		intron_variant	Intron 1 of 2
ENSG00000289052	ENST00000726370.1	n.261+10133A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0870 AC: 13243 AN: 152154 Hom.: 733 Cov.: 33

Gnomad AFR AF: 0.0240

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.0813

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.0518

Gnomad SAS AF: 0.0836

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.0936

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

GnomAD4 genome AF: 0.0870 AC: 13242 AN: 152272 Hom.: 734 Cov.: 33 AF XY: 0.0855 AC XY: 6365 AN XY: 74470

African (AFR) AF: 0.0240 AC: 995 AN: 41540

American (AMR) AF: 0.0812 AC: 1243 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 389 AN: 3468

East Asian (EAS) AF: 0.0521 AC: 270 AN: 5186

South Asian (SAS) AF: 0.0832 AC: 402 AN: 4830

European-Finnish (FIN) AF: 0.101 AC: 1076 AN: 10606

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8579 AN: 68018

Other (OTH) AF: 0.0926 AC: 196 AN: 2116

Alfa AF: 0.113 Hom.: 1916

Bravo AF: 0.0826

Asia WGS AF: 0.0700 AC: 242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.9
DANN	Benign	0.43
PhyloP100		0.070

Splicing

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

Other links and lift over

dbSNP: rs2215564; hg19: chr7-150563964;