rs6945082

Variant names:

• chr7-54890765-G-A
• rs6945082
• ENST00000795375.1:n.164-3432C>T

Variant summary

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

The ENST00000795375.1(ENSG00000303536):​n.164-3432C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 151,962 control chromosomes in the GnomAD database, including 5,351 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 0.25 (5351 hom., cov: 33)
• Consequence: ENSG00000303536 ENST00000795375.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500
• Publications: 5 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.307 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
ENSG00000303536	ENST00000795375.1	n.164-3432C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38675 AN: 151844 Hom.: 5353 Cov.: 33

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.0199

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.254 AC: 38669 AN: 151962 Hom.: 5351 Cov.: 33 AF XY: 0.248 AC XY: 18394 AN XY: 74288

African (AFR) AF: 0.203 AC: 8396 AN: 41460

American (AMR) AF: 0.224 AC: 3427 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1114 AN: 3468

East Asian (EAS) AF: 0.0199 AC: 103 AN: 5168

South Asian (SAS) AF: 0.177 AC: 854 AN: 4816

European-Finnish (FIN) AF: 0.243 AC: 2562 AN: 10550

Middle Eastern (MID) AF: 0.363 AC: 103 AN: 284

European-Non Finnish (NFE) AF: 0.311 AC: 21102 AN: 67918

Other (OTH) AF: 0.287 AC: 605 AN: 2108

Alfa AF: 0.294 Hom.: 21542

Bravo AF: 0.251

Asia WGS AF: 0.0860 AC: 297 AN: 3436

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.1
DANN	Benign	0.25
PhyloP100		-0.050

Splicing

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

Other links and lift over

dbSNP: rs6945082; hg19: chr7-54958458;