7-12883931-T-C

Position:

• chr7-12883931-T-C

Variant summary

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

The ENST00000638964.1(ENSG00000229618):​n.484+81199T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 151,728 control chromosomes in the GnomAD database, including 24,950 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 0.56 (24950 hom., cov: 30)
• Consequence: ENSG00000229618 ENST00000638964.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.92

Genes affected

ENSG00000229618 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000229618	ENST00000638964.1	n.484+81199T>C		intron_variant		5
ENSG00000229618	ENST00000639998.1	n.483+125615T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.560 AC: 84853 AN: 151610 Hom.: 24918 Cov.: 30

Gnomad AFR AF: 0.765

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.558

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

GnomAD4 genome AF: 0.560 AC: 84920 AN: 151728 Hom.: 24950 Cov.: 30 AF XY: 0.561 AC XY: 41578 AN XY: 74100

Gnomad4 AFR AF: 0.765

Gnomad4 AMR AF: 0.506

Gnomad4 ASJ AF: 0.453

Gnomad4 EAS AF: 0.490

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.519

Gnomad4 NFE AF: 0.474

Gnomad4 OTH AF: 0.554

Alfa AF: 0.513 Hom.: 2492

Bravo AF: 0.565

Asia WGS AF: 0.523 AC: 1816 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.35
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6460985; hg19: chr7-12923556;