rs7164700

Variant names:

• chr15-48018144-G-A
• rs7164700
• ENST00000560900.1:n.258+25373G>A

Variant summary

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

The ENST00000560900.1(ENSG00000259754):​n.258+25373G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0854 in 152,174 control chromosomes in the GnomAD database, including 998 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 0.085 (998 hom., cov: 32)
• Consequence: ENSG00000259754 ENST00000560900.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.415
• Publications: 0 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900354	XR_001751516.3	n.205+25373G>A		intron_variant	Intron 2 of 2
LOC124900354	XR_001751518.3	n.145+25373G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259754	ENST00000560900.1	n.258+25373G>A		intron_variant	Intron 2 of 2	4
ENSG00000259754	ENST00000662551.1	n.251+25373G>A		intron_variant	Intron 2 of 2
ENSG00000259754	ENST00000665188.1	n.220+19989G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0852 AC: 12954 AN: 152056 Hom.: 992 Cov.: 32

Gnomad AFR AF: 0.0914

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.0842

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.0317

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0545

Gnomad OTH AF: 0.0981

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

GnomAD4 genome AF: 0.0854 AC: 12992 AN: 152174 Hom.: 998 Cov.: 32 AF XY: 0.0873 AC XY: 6494 AN XY: 74388

African (AFR) AF: 0.0917 AC: 3807 AN: 41522

American (AMR) AF: 0.116 AC: 1778 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0842 AC: 292 AN: 3468

East Asian (EAS) AF: 0.440 AC: 2269 AN: 5162

South Asian (SAS) AF: 0.116 AC: 556 AN: 4812

European-Finnish (FIN) AF: 0.0317 AC: 336 AN: 10604

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0545 AC: 3709 AN: 68008

Other (OTH) AF: 0.104 AC: 219 AN: 2112

Alfa AF: 0.0622 Hom.: 128

Bravo AF: 0.0936

Asia WGS AF: 0.298 AC: 1033 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.5
DANN	Benign	0.73
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs7164700; hg19: chr15-48310341;