rs987252

chr7-51625070-A-Gchr7-51625070-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, non coding transcript 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: ENST00000414409.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.39

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000414409.1	n.397-5609A>G		intron_variant, non_coding_transcript_variant		4
	ENST00000648455.1	n.353-39638A>G		intron_variant, non_coding_transcript_variant

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;