rs987252

Variant names:

• chr7-51625070-A-G
• rs987252
• ENST00000414409.2:n.397-5609A>G

Your query was ambiguous. Multiple possible variants found:

• chr7-51625070-A-G
• chr7-51625070-A-T

Variant summary

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

The ENST00000414409.2(ENSG00000285741):​n.397-5609A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.588 in 151,634 control chromosomes in the GnomAD database, including 26,304 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 0.59 (26304 hom., cov: 30)
• Consequence: ENSG00000285741 ENST00000414409.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.39
• Publications: 2 publications found

Genes affected

ENSG00000285741 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000414409.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285741	ENST00000414409.2	TSL:4	n.397-5609A>G		intron	N/A
	ENSG00000285741	ENST00000648455.1		n.353-39638A>G		intron	N/A
	ENSG00000285741	ENST00000769890.1		n.481-39638A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.588 AC: 89082 AN: 151514 Hom.: 26275 Cov.: 30

Gnomad AFR AF: 0.635

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.612

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.588 AC: 89164 AN: 151634 Hom.: 26304 Cov.: 30 AF XY: 0.592 AC XY: 43829 AN XY: 74048

African (AFR) AF: 0.635 AC: 26244 AN: 41326

American (AMR) AF: 0.558 AC: 8492 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 2199 AN: 3468

East Asian (EAS) AF: 0.613 AC: 3153 AN: 5144

South Asian (SAS) AF: 0.641 AC: 3077 AN: 4802

European-Finnish (FIN) AF: 0.574 AC: 6014 AN: 10472

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.562 AC: 38126 AN: 67892

Other (OTH) AF: 0.577 AC: 1212 AN: 2102

Alfa AF: 0.571 Hom.: 92342

Bravo AF: 0.584

Asia WGS AF: 0.629 AC: 2184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.69
DANN	Benign	0.71
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs987252; hg19: chr7-51692766;