rs987252

Variant names:

• chr7-51625070-A-G
• rs987252
• ENST00000414409.1: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. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000414409.1(ENSG00000229403):​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: ENSG00000229403 ENST00000414409.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.39

Genes affected

ENSG00000229403 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000229403	ENST00000414409.1	n.397-5609A>G		intron_variant	Intron 1 of 1	4
ENSG00000285741	ENST00000648455.1	n.353-39638A>G		intron_variant	Intron 2 of 6

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

Gnomad4 AFR AF: 0.635

Gnomad4 AMR AF: 0.558

Gnomad4 ASJ AF: 0.634

Gnomad4 EAS AF: 0.613

Gnomad4 SAS AF: 0.641

Gnomad4 FIN AF: 0.574

Gnomad4 NFE AF: 0.562

Gnomad4 OTH AF: 0.577

Alfa AF: 0.566 Hom.: 44321

Bravo AF: 0.584

Asia WGS AF: 0.629 AC: 2184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs987252; hg19: chr7-51692766;