rs2850889

Variant names:

• chr18-77246651-T-C
• rs2850889
• ENST00000844037.1:n.162+4197A>G

Variant summary

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

The ENST00000844037.1(ENSG00000309801):​n.162+4197A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 151,960 control chromosomes in the GnomAD database, including 12,662 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 0.40 (12662 hom., cov: 31)
• Consequence: ENSG00000309801 ENST00000844037.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330
• Publications: 6 publications found

Genes affected

ENSG00000309801 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.454 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
ENSG00000309801	ENST00000844037.1	n.162+4197A>G		intron_variant	Intron 1 of 1
ENSG00000309801	ENST00000844038.1	n.118+4150A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.402 AC: 61111 AN: 151842 Hom.: 12651 Cov.: 31

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.402 AC: 61149 AN: 151960 Hom.: 12662 Cov.: 31 AF XY: 0.400 AC XY: 29693 AN XY: 74278

African (AFR) AF: 0.351 AC: 14541 AN: 41444

American (AMR) AF: 0.334 AC: 5101 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1819 AN: 3464

East Asian (EAS) AF: 0.279 AC: 1443 AN: 5166

South Asian (SAS) AF: 0.323 AC: 1554 AN: 4818

European-Finnish (FIN) AF: 0.400 AC: 4210 AN: 10538

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.458 AC: 31132 AN: 67956

Other (OTH) AF: 0.407 AC: 859 AN: 2112

Alfa AF: 0.439 Hom.: 62938

Bravo AF: 0.395

Asia WGS AF: 0.294 AC: 1023 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.4
DANN	Benign	0.83
PhyloP100		-0.033

Splicing

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

Other links and lift over

dbSNP: rs2850889; hg19: chr18-74958607;