rs7000280

Variant names:

• chr8-26698423-T-C
• rs7000280
• ENST00000792407.1:n.85+27549T>C

Variant summary

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

The ENST00000792407.1(ENSG00000303169):​n.85+27549T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 152,130 control chromosomes in the GnomAD database, including 3,205 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 0.20 (3205 hom., cov: 32)
• Consequence: ENSG00000303169 ENST00000792407.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.707
• Publications: 1 publications found

Genes affected

ENSG00000303169 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.262 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
ENSG00000303169	ENST00000792407.1	n.85+27549T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30231 AN: 152012 Hom.: 3207 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.165

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.199 AC: 30251 AN: 152130 Hom.: 3205 Cov.: 32 AF XY: 0.196 AC XY: 14555 AN XY: 74364

African (AFR) AF: 0.266 AC: 11032 AN: 41476

American (AMR) AF: 0.142 AC: 2163 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 493 AN: 3466

East Asian (EAS) AF: 0.250 AC: 1294 AN: 5180

South Asian (SAS) AF: 0.112 AC: 540 AN: 4818

European-Finnish (FIN) AF: 0.186 AC: 1965 AN: 10592

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12238 AN: 67998

Other (OTH) AF: 0.158 AC: 334 AN: 2114

Alfa AF: 0.202 Hom.: 423

Bravo AF: 0.199

Asia WGS AF: 0.169 AC: 589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.2
DANN	Benign	0.56
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs7000280; hg19: chr8-26555940;