7-12800465-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

Genes affected

ENSG00000229618 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000639998.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000229618	ENST00000639998.1	TSL:5	n.483+42149T>C		intron	N/A

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

African (AFR) AF: 0.272 AC: 11285 AN: 41456

American (AMR) AF: 0.425 AC: 6489 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1221 AN: 3468

East Asian (EAS) AF: 0.376 AC: 1931 AN: 5140

South Asian (SAS) AF: 0.474 AC: 2287 AN: 4820

European-Finnish (FIN) AF: 0.386 AC: 4073 AN: 10546

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29558 AN: 67972

Other (OTH) AF: 0.389 AC: 820 AN: 2108

Alfa AF: 0.405 Hom.: 7149

Bravo AF: 0.378

Asia WGS AF: 0.408 AC: 1417 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	13
DANN	Benign	0.74
PhyloP100		3.8

Splicing

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

Other links and lift over

dbSNP: rs7792487; hg19: chr7-12840090;