5-120069960-C-T

Variant names:

• chr5-120069960-C-T
• rs6878265
• ENST00000795145.1:n.195+8923G>A

Variant summary

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

The ENST00000795145.1(ENSG00000303506):​n.195+8923G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 151,848 control chromosomes in the GnomAD database, including 9,460 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 0.29 (9460 hom., cov: 32)
• Consequence: ENSG00000303506 ENST00000795145.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.339
• Publications: 3 publications found

Genes affected

ENSG00000303506 (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 (AFR) allele frequency at 95% confidence interval = 0.598 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
ENSG00000303506	ENST00000795145.1	n.195+8923G>A		intron_variant	Intron 1 of 3
ENSG00000303506	ENST00000795146.1	n.195+8923G>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43898 AN: 151730 Hom.: 9439 Cov.: 32

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.290 AC: 43965 AN: 151848 Hom.: 9460 Cov.: 32 AF XY: 0.290 AC XY: 21503 AN XY: 74182

African (AFR) AF: 0.605 AC: 25041 AN: 41406

American (AMR) AF: 0.208 AC: 3172 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 462 AN: 3468

East Asian (EAS) AF: 0.315 AC: 1621 AN: 5150

South Asian (SAS) AF: 0.251 AC: 1212 AN: 4828

European-Finnish (FIN) AF: 0.164 AC: 1735 AN: 10554

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10066 AN: 67880

Other (OTH) AF: 0.260 AC: 548 AN: 2108

Alfa AF: 0.248 Hom.: 1212

Bravo AF: 0.304

Asia WGS AF: 0.332 AC: 1146 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.40
DANN	Benign	0.18
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs6878265; hg19: chr5-119405655;