rs2948998

Variant names:

• chr8-110286314-G-A
• rs2948998
• ENST00000817559.1:n.321-4709G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-110286314-G-A
• chr8-110286314-G-C

Variant summary

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

The ENST00000817559.1(ENSG00000306390):​n.321-4709G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 151,928 control chromosomes in the GnomAD database, including 21,208 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 0.51 (21208 hom., cov: 32)
• Consequence: ENSG00000306390 ENST00000817559.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.263
• Publications: 1 publications found

Genes affected

ENSG00000306390 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.625 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
ENSG00000306390	ENST00000817559.1	n.321-4709G>A		intron_variant	Intron 2 of 2
ENSG00000306390	ENST00000817562.1	n.269-666G>A		intron_variant	Intron 2 of 3
ENSG00000306390	ENST00000817563.1	n.429+264G>A		intron_variant	Intron 4 of 5
ENSG00000306390	ENST00000817564.1	n.208+264G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.514 AC: 77958 AN: 151810 Hom.: 21193 Cov.: 32

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.644

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.513 AC: 78007 AN: 151928 Hom.: 21208 Cov.: 32 AF XY: 0.515 AC XY: 38238 AN XY: 74244

African (AFR) AF: 0.335 AC: 13900 AN: 41440

American (AMR) AF: 0.492 AC: 7517 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.570 AC: 1974 AN: 3466

East Asian (EAS) AF: 0.644 AC: 3323 AN: 5162

South Asian (SAS) AF: 0.586 AC: 2814 AN: 4806

European-Finnish (FIN) AF: 0.600 AC: 6314 AN: 10522

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.594 AC: 40381 AN: 67952

Other (OTH) AF: 0.527 AC: 1112 AN: 2112

Alfa AF: 0.561 Hom.: 78895

Bravo AF: 0.492

Asia WGS AF: 0.598 AC: 2079 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	0.16
DANN	Benign	0.39
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs2948998; hg19: chr8-111298543;