chr7-12883931-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000229618	ENST00000638964.1	n.484+81199T>C		intron_variant	Intron 1 of 5	5
ENSG00000229618	ENST00000639998.1	n.483+125615T>C		intron_variant	Intron 3 of 7	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;