rs7508868

Variant names:

• chr20-7674279-C-T
• rs7508868
• ENST00000839999.1:n.397-5280G>A

Variant summary

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

The ENST00000839999.1(ENSG00000309276):​n.397-5280G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0137 in 152,180 control chromosomes in the GnomAD database, including 24 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 0.014 (24 hom., cov: 33)
• Consequence: ENSG00000309276 ENST00000839999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105
• Publications: 1 publications found

Genes affected

ENSG00000309276 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0137 (2082/152180) while in subpopulation NFE AF = 0.0183 (1242/68004). AF 95% confidence interval is 0.0174. There are 24 homozygotes in GnomAd4. There are 1039 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 24 gene

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
ENSG00000309276	ENST00000839999.1	n.397-5280G>A		intron_variant	Intron 3 of 4
ENSG00000309276	ENST00000840000.1	n.76-5280G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0137 AC: 2081 AN: 152062 Hom.: 22 Cov.: 33

Gnomad AFR AF: 0.00331

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0164

Gnomad ASJ AF: 0.0369

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0154

Gnomad FIN AF: 0.0189

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0183

Gnomad OTH AF: 0.0196

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

GnomAD4 genome AF: 0.0137 AC: 2082 AN: 152180 Hom.: 24 Cov.: 33 AF XY: 0.0140 AC XY: 1039 AN XY: 74394

African (AFR) AF: 0.00330 AC: 137 AN: 41530

American (AMR) AF: 0.0164 AC: 250 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0369 AC: 128 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5174

South Asian (SAS) AF: 0.0160 AC: 77 AN: 4814

European-Finnish (FIN) AF: 0.0189 AC: 200 AN: 10590

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0183 AC: 1242 AN: 68004

Other (OTH) AF: 0.0194 AC: 41 AN: 2116

Alfa AF: 0.0182 Hom.: 35

Bravo AF: 0.0124

Asia WGS AF: 0.00635 AC: 22 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.9
DANN	Benign	0.33
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs7508868; hg19: chr20-7654926;