rs2934177

Variant names:

• chr15-47921350-C-T
• rs2934177
• ENST00000560900.1:n.195+36846C>T

Variant summary

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

The ENST00000560900.1(ENSG00000259754):​n.195+36846C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.975 in 152,226 control chromosomes in the GnomAD database, including 72,555 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 0.97 (72555 hom., cov: 33)
• Consequence: ENSG00000259754 ENST00000560900.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66
• 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.98 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900354	XR_001751516.3	n.142+36846C>T		intron_variant	Intron 1 of 2
LOC124900354	XR_001751517.2	n.142+36846C>T		intron_variant	Intron 1 of 2
LOC124900354	XR_001751518.3	n.82+5988C>T		intron_variant	Intron 1 of 2
LOC124900354	XR_007064618.1	n.143-28006C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259754	ENST00000560900.1	n.195+36846C>T		intron_variant	Intron 1 of 2	4
ENSG00000259754	ENST00000662551.1	n.189-71359C>T		intron_variant	Intron 1 of 2
ENSG00000259754	ENST00000664705.1	n.189-71359C>T		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.975 AC: 148259 AN: 152102 Hom.: 72496 Cov.: 33

Gnomad AFR AF: 0.987

Gnomad AMI AF: 0.988

Gnomad AMR AF: 0.961

Gnomad ASJ AF: 0.979

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.979

Gnomad FIN AF: 0.986

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.986

Gnomad OTH AF: 0.974

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

GnomAD4 genome AF: 0.975 AC: 148380 AN: 152226 Hom.: 72555 Cov.: 33 AF XY: 0.973 AC XY: 72421 AN XY: 74422

African (AFR) AF: 0.987 AC: 41040 AN: 41582

American (AMR) AF: 0.961 AC: 14707 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.979 AC: 3399 AN: 3472

East Asian (EAS) AF: 0.725 AC: 3669 AN: 5062

South Asian (SAS) AF: 0.979 AC: 4727 AN: 4828

European-Finnish (FIN) AF: 0.986 AC: 10473 AN: 10622

Middle Eastern (MID) AF: 0.986 AC: 290 AN: 294

European-Non Finnish (NFE) AF: 0.986 AC: 67113 AN: 68038

Other (OTH) AF: 0.974 AC: 2061 AN: 2116

Alfa AF: 0.984 Hom.: 9296

Bravo AF: 0.972

Asia WGS AF: 0.892 AC: 3092 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.040
DANN	Benign	0.68
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs2934177; hg19: chr15-48213547;