7-45361296-C-T

Variant names:

• chr7-45361296-C-T
• rs1852612
• ENST00000666999.1:n.838-23404C>T

Variant summary

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

The ENST00000666999.1(ENSG00000286738):​n.838-23404C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.437 in 151,958 control chromosomes in the GnomAD database, including 15,575 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 0.44 (15575 hom., cov: 32)
• Consequence: ENSG00000286738 ENST00000666999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04

Genes affected

ENSG00000286738 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.603 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
ENSG00000286738	ENST00000666999.1	n.838-23404C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66242 AN: 151840 Hom.: 15528 Cov.: 32

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.437 AC: 66346 AN: 151958 Hom.: 15575 Cov.: 32 AF XY: 0.432 AC XY: 32099 AN XY: 74268

Gnomad4 AFR AF: 0.610

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.495

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.373

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.448

Alfa AF: 0.390 Hom.: 5333

Bravo AF: 0.446

Asia WGS AF: 0.330 AC: 1149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.058
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1852612; hg19: chr7-45400895;