rs1478959

Variant names:

• chr8-2202103-C-A
• rs1478959
• ENST00000776944.1:n.1027C>A

Variant summary

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

The ENST00000776944.1(ENSG00000288782):​n.1027C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,072 control chromosomes in the GnomAD database, including 3,519 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 0.21 (3519 hom., cov: 33)
• Consequence: ENSG00000288782 ENST00000776944.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67
• Publications: 2 publications found

Genes affected

ENSG00000288782 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.26 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
ENSG00000288782	ENST00000776944.1	n.1027C>A		non_coding_transcript_exon_variant	Exon 5 of 5
ENSG00000288782	ENST00000776942.1	n.211-970C>A		intron_variant	Intron 2 of 3
ENSG00000288782	ENST00000776943.1	n.452-970C>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31162 AN: 151952 Hom.: 3513 Cov.: 33

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.0701

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.205 AC: 31201 AN: 152072 Hom.: 3519 Cov.: 33 AF XY: 0.196 AC XY: 14545 AN XY: 74334

African (AFR) AF: 0.264 AC: 10949 AN: 41498

American (AMR) AF: 0.158 AC: 2407 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 659 AN: 3460

East Asian (EAS) AF: 0.0702 AC: 364 AN: 5182

South Asian (SAS) AF: 0.129 AC: 618 AN: 4794

European-Finnish (FIN) AF: 0.115 AC: 1213 AN: 10586

Middle Eastern (MID) AF: 0.199 AC: 58 AN: 292

European-Non Finnish (NFE) AF: 0.210 AC: 14268 AN: 67972

Other (OTH) AF: 0.211 AC: 444 AN: 2104

Alfa AF: 0.215 Hom.: 429

Bravo AF: 0.212

Asia WGS AF: 0.0990 AC: 343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.14
DANN	Benign	0.14
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1478959; hg19: chr8-2149742;