7-12892424-G-T

Variant names:

• chr7-12892424-G-T
• rs732577
• ENST00000638964.1:n.484+89692G>T

Variant summary

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

The ENST00000638964.1(ENSG00000229618):​n.484+89692G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 152,068 control chromosomes in the GnomAD database, including 16,072 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 0.45 (16072 hom., cov: 32)
• Consequence: ENSG00000229618 ENST00000638964.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.675

Genes affected

ENSG00000229618 (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 (NFE) allele frequency at 95% confidence interval = 0.514 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
ENSG00000229618	ENST00000638964.1	n.484+89692G>T		intron_variant	Intron 1 of 5	5
ENSG00000229618	ENST00000639998.1	n.483+134108G>T		intron_variant	Intron 3 of 7	5

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68689 AN: 151950 Hom.: 16060 Cov.: 32

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.452 AC: 68730 AN: 152068 Hom.: 16072 Cov.: 32 AF XY: 0.443 AC XY: 32956 AN XY: 74336

Gnomad4 AFR AF: 0.352

Gnomad4 AMR AF: 0.510

Gnomad4 ASJ AF: 0.488

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.403

Gnomad4 FIN AF: 0.391

Gnomad4 NFE AF: 0.519

Gnomad4 OTH AF: 0.500

Alfa AF: 0.501 Hom.: 27591

Bravo AF: 0.457

Asia WGS AF: 0.332 AC: 1157 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	0.36
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs732577; hg19: chr7-12932049;