rs7792487

Variant names:

• chr7-12800465-T-C
• rs7792487
• ENST00000639998.1:n.483+42149T>C

Your query was ambiguous. Multiple possible variants found:

• chr7-12800465-T-C
• chr7-12800465-T-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000639998.1(ENSG00000229618):​n.483+42149T>C variant causes a intron change. The variant allele was found at a frequency of 0.383 in 151,976 control chromosomes in the GnomAD database, including 11,477 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 0.38 (11477 hom., cov: 32)
• Consequence: ENSG00000229618 ENST00000639998.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.83

Genes affected

ENSG00000229618 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.458 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	ENST00000639998.1	n.483+42149T>C		intron_variant	Intron 3 of 7	5

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58151 AN: 151860 Hom.: 11479 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.383 AC: 58181 AN: 151976 Hom.: 11477 Cov.: 32 AF XY: 0.382 AC XY: 28336 AN XY: 74268

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.376

Gnomad4 SAS AF: 0.474

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.435

Gnomad4 OTH AF: 0.389

Alfa AF: 0.404 Hom.: 6433

Bravo AF: 0.378

Asia WGS AF: 0.408 AC: 1417 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	13
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7792487; hg19: chr7-12840090;