rs7147817

Variant names:

• chr14-40362800-A-G
• rs7147817
• ENST00000553464.2:n.501-23452A>G

Variant summary

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

The ENST00000553464.2(ENSG00000258526):​n.501-23452A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 151,940 control chromosomes in the GnomAD database, including 18,117 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 0.48 (18117 hom., cov: 31)
• Consequence: ENSG00000258526 ENST00000553464.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.82
• Publications: 3 publications found

Genes affected

ENSG00000258526 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370462	XR_007064129.1	n.196-8721A>G		intron_variant	Intron 1 of 2
LOC105370462	XR_943784.3	n.192-8721A>G		intron_variant	Intron 1 of 4
LOC105370462	XR_943785.3	n.729+6816A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000258526	ENST00000553464.2	n.501-23452A>G		intron_variant	Intron 5 of 7	5
ENSG00000258526	ENST00000652126.1	n.643-8721A>G		intron_variant	Intron 5 of 7
ENSG00000258526	ENST00000663500.1	n.481-23452A>G		intron_variant	Intron 5 of 7

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72927 AN: 151822 Hom.: 18111 Cov.: 31

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.619

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.480 AC: 72957 AN: 151940 Hom.: 18117 Cov.: 31 AF XY: 0.478 AC XY: 35529 AN XY: 74260

African (AFR) AF: 0.389 AC: 16113 AN: 41414

American (AMR) AF: 0.502 AC: 7665 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.567 AC: 1965 AN: 3466

East Asian (EAS) AF: 0.307 AC: 1582 AN: 5158

South Asian (SAS) AF: 0.342 AC: 1653 AN: 4828

European-Finnish (FIN) AF: 0.576 AC: 6080 AN: 10554

Middle Eastern (MID) AF: 0.534 AC: 156 AN: 292

European-Non Finnish (NFE) AF: 0.532 AC: 36146 AN: 67952

Other (OTH) AF: 0.490 AC: 1035 AN: 2114

Alfa AF: 0.506 Hom.: 53870

Bravo AF: 0.470

Asia WGS AF: 0.317 AC: 1100 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.1
DANN	Benign	0.38
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs7147817; hg19: chr14-40832004;