rs7677217

Variant names:

• chr4-23715016-G-A
• rs7677217
• ENST00000514290.1:n.118-53303G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000514290.1(ENSG00000250137):​n.118-53303G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.403 in 151,510 control chromosomes in the GnomAD database, including 13,432 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 0.40 (13432 hom., cov: 31)
• Consequence: ENSG00000250137 ENST00000514290.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.59

Genes affected

ENSG00000250137 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.495 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
ENSG00000250137	ENST00000514290.1	n.118-53303G>A		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.403 AC: 61044 AN: 151394 Hom.: 13434 Cov.: 31

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.403 AC: 61052 AN: 151510 Hom.: 13432 Cov.: 31 AF XY: 0.400 AC XY: 29574 AN XY: 73980

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.416

Gnomad4 ASJ AF: 0.516

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.347

Gnomad4 FIN AF: 0.475

Gnomad4 NFE AF: 0.499

Gnomad4 OTH AF: 0.427

Alfa AF: 0.448 Hom.: 2561

Bravo AF: 0.393

Asia WGS AF: 0.298 AC: 1039 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	17
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7677217; hg19: chr4-23716639;