chr8-2797033-C-A

Variant names:

• chr8-2797033-C-A
• rs1026374
• ENST00000520024.1:n.177-7553C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000520024.1(ENSG00000253853):​n.177-7553C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00821 in 152,040 control chromosomes in the GnomAD database, including 17 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 0.0082 (17 hom., cov: 31)
• Consequence: ENSG00000253853 ENST00000520024.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• Publications: 2 publications found

Genes affected

ENSG00000253853 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00821 (1249/152040) while in subpopulation AFR AF = 0.0247 (1022/41454). AF 95% confidence interval is 0.0234. There are 17 homozygotes in GnomAd4. There are 609 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 17 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377785	NR_168441.1	n.539-7553C>A		intron_variant	Intron 1 of 11
LOC105377785	NR_168442.1	n.539-7553C>A		intron_variant	Intron 1 of 14
LOC105377785	NR_168443.1	n.539-7553C>A		intron_variant	Intron 1 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253853	ENST00000520024.1	n.177-7553C>A		intron_variant	Intron 1 of 4	3
ENSG00000253853	ENST00000654515.1	n.532-7553C>A		intron_variant	Intron 1 of 5
ENSG00000253853	ENST00000662575.1	n.81+1658C>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.00821 AC: 1247 AN: 151926 Hom.: 17 Cov.: 31

Gnomad AFR AF: 0.0247

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00917

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0159

Gnomad NFE AF: 0.000956

Gnomad OTH AF: 0.00813

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

GnomAD4 genome AF: 0.00821 AC: 1249 AN: 152040 Hom.: 17 Cov.: 31 AF XY: 0.00819 AC XY: 609 AN XY: 74326

African (AFR) AF: 0.0247 AC: 1022 AN: 41454

American (AMR) AF: 0.00916 AC: 140 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5152

South Asian (SAS) AF: 0.00 AC: 0 AN: 4816

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10564

Middle Eastern (MID) AF: 0.0171 AC: 5 AN: 292

European-Non Finnish (NFE) AF: 0.000956 AC: 65 AN: 67988

Other (OTH) AF: 0.00805 AC: 17 AN: 2112

Alfa AF: 0.0000444 Hom.: 4326

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.21
DANN	Benign	0.48
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1026374; hg19: chr8-2654569;