rs998124

Variant names:

• chr18-45145697-A-G
• rs998124
• ENST00000589845.7:n.445+4443T>C

Your query was ambiguous. Multiple possible variants found:

• chr18-45145697-A-G
• chr18-45145697-A-T

Variant summary

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

The ENST00000589845.7(ENSG00000267101):​n.445+4443T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,118 control chromosomes in the GnomAD database, including 1,520 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 0.12 (1520 hom., cov: 31)
• Consequence: ENSG00000267101 ENST00000589845.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.30
• Publications: 14 publications found

Genes affected

ENSG00000267101 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372091	XR_007066349.1	n.216+4443T>C		intron_variant	Intron 2 of 3
LOC105372091	XR_935421.3	n.216+4443T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000267101	ENST00000589845.7	n.445+4443T>C		intron_variant	Intron 3 of 3	2
ENSG00000267101	ENST00000658735.1	n.438+4443T>C		intron_variant	Intron 3 of 4
ENSG00000267101	ENST00000660208.1	n.588+4443T>C		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18714 AN: 152000 Hom.: 1518 Cov.: 31

Gnomad AFR AF: 0.0298

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.0610

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.123 AC: 18707 AN: 152118 Hom.: 1520 Cov.: 31 AF XY: 0.122 AC XY: 9072 AN XY: 74358

African (AFR) AF: 0.0297 AC: 1235 AN: 41550

American (AMR) AF: 0.113 AC: 1724 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 700 AN: 3460

East Asian (EAS) AF: 0.0607 AC: 315 AN: 5186

South Asian (SAS) AF: 0.169 AC: 814 AN: 4812

European-Finnish (FIN) AF: 0.152 AC: 1608 AN: 10594

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11889 AN: 67940

Other (OTH) AF: 0.123 AC: 259 AN: 2110

Alfa AF: 0.155 Hom.: 6321

Bravo AF: 0.112

Asia WGS AF: 0.0940 AC: 326 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.1
DANN	Benign	0.59
PhyloP100		2.3

Splicing

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

Other links and lift over

dbSNP: rs998124; hg19: chr18-42725662;