rs1994198

Variant names:

• chr15-46360969-C-T
• rs1994198
• ENST00000811159.1:n.204-13504C>T

Variant summary

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

The ENST00000811159.1(ENSG00000305466):​n.204-13504C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 151,554 control chromosomes in the GnomAD database, including 17,977 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 0.47 (17977 hom., cov: 31)
• Consequence: ENSG00000305466 ENST00000811159.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.780
• Publications: 9 publications found

Genes affected

ENSG00000305466 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.556 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
ENSG00000305466	ENST00000811159.1	n.204-13504C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.473 AC: 71657 AN: 151436 Hom.: 17979 Cov.: 31

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.637

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.473 AC: 71683 AN: 151554 Hom.: 17977 Cov.: 31 AF XY: 0.468 AC XY: 34606 AN XY: 73998

African (AFR) AF: 0.360 AC: 14899 AN: 41380

American (AMR) AF: 0.421 AC: 6386 AN: 15164

Ashkenazi Jewish (ASJ) AF: 0.613 AC: 2121 AN: 3458

East Asian (EAS) AF: 0.230 AC: 1179 AN: 5128

South Asian (SAS) AF: 0.425 AC: 2047 AN: 4812

European-Finnish (FIN) AF: 0.504 AC: 5299 AN: 10520

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.560 AC: 37980 AN: 67780

Other (OTH) AF: 0.482 AC: 1017 AN: 2108

Alfa AF: 0.519 Hom.: 5894

Bravo AF: 0.463

Asia WGS AF: 0.307 AC: 1066 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.50
DANN	Benign	0.34
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs1994198; hg19: chr15-46653167;