ENST00000795375.1:n.211-12382C>T

Variant names:

• chr7-54824378-G-A
• rs9691864
• ENST00000795375.1:n.211-12382C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000795375.1(ENSG00000303536):​n.211-12382C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 151,736 control chromosomes in the GnomAD database, including 7,583 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 0.30 (7583 hom., cov: 31)
• Consequence: ENSG00000303536 ENST00000795375.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.789
• Publications: 2 publications found

Genes affected

ENSG00000303536 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000795375.1. 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
	ENSG00000303536	ENST00000795375.1		n.211-12382C>T		intron	N/A
	ENSG00000303536	ENST00000795376.1		n.147-12382C>T		intron	N/A
	ENSG00000303536	ENST00000795377.1		n.274-12382C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45762 AN: 151618 Hom.: 7589 Cov.: 31

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.0738

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.302 AC: 45764 AN: 151736 Hom.: 7583 Cov.: 31 AF XY: 0.295 AC XY: 21879 AN XY: 74148

African (AFR) AF: 0.189 AC: 7805 AN: 41348

American (AMR) AF: 0.333 AC: 5066 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1327 AN: 3466

East Asian (EAS) AF: 0.0739 AC: 381 AN: 5154

South Asian (SAS) AF: 0.296 AC: 1416 AN: 4790

European-Finnish (FIN) AF: 0.269 AC: 2830 AN: 10506

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.379 AC: 25735 AN: 67920

Other (OTH) AF: 0.327 AC: 690 AN: 2112

Alfa AF: 0.362 Hom.: 16858

Bravo AF: 0.299

Asia WGS AF: 0.182 AC: 632 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	4.0
DANN	Benign	0.87
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs9691864; hg19: chr7-54892071;