rs1842908

Variant names:

• chr11-18929590-C-T
• rs1842908
• ENST00000836338.1:n.374-9715C>T

Variant summary

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

The ENST00000836338.1(ENSG00000255244):​n.374-9715C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.963 in 151,494 control chromosomes in the GnomAD database, including 70,545 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 0.96 (70545 hom., cov: 39)
• Consequence: ENSG00000255244 ENST00000836338.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.728
• Publications: 3 publications found

Genes affected

ENSG00000255244 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 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
ENSG00000255244	ENST00000836338.1	n.374-9715C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.963 AC: 145724 AN: 151376 Hom.: 70486 Cov.: 39

Gnomad AFR AF: 0.869

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.988

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.994

Gnomad NFE AF: 1.00

Gnomad OTH AF: 0.972

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

GnomAD4 genome AF: 0.963 AC: 145843 AN: 151494 Hom.: 70545 Cov.: 39 AF XY: 0.964 AC XY: 71362 AN XY: 74012

African (AFR) AF: 0.870 AC: 35975 AN: 41360

American (AMR) AF: 0.988 AC: 14935 AN: 15112

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3466 AN: 3466

East Asian (EAS) AF: 1.00 AC: 5152 AN: 5152

South Asian (SAS) AF: 1.00 AC: 4763 AN: 4764

European-Finnish (FIN) AF: 1.00 AC: 10550 AN: 10550

Middle Eastern (MID) AF: 0.990 AC: 289 AN: 292

European-Non Finnish (NFE) AF: 1.00 AC: 67761 AN: 67788

Other (OTH) AF: 0.972 AC: 2040 AN: 2098

Alfa AF: 0.978 Hom.: 82551

Asia WGS AF: 0.994 AC: 3444 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.35
DANN	Benign	0.38
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs1842908; hg19: chr11-18951137;