rs9947485

Variant names:

• chr18-77180899-C-T
• rs9947485
• ENST00000584843.1:n.95+699C>T

Variant summary

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

The ENST00000584843.1(ENSG00000265844):​n.95+699C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 152,154 control chromosomes in the GnomAD database, including 1,661 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 0.14 (1661 hom., cov: 32)
• Consequence: ENSG00000265844 ENST00000584843.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.39
• Publications: 4 publications found

Genes affected

ENSG00000265844 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.161 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
ENSG00000265844	ENST00000584843.1	n.95+699C>T		intron_variant	Intron 1 of 4	4
ENSG00000265844	ENST00000843890.1	n.301-4285C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21613 AN: 152036 Hom.: 1655 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.0804

Gnomad EAS AF: 0.0739

Gnomad SAS AF: 0.0820

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.142 AC: 21648 AN: 152154 Hom.: 1661 Cov.: 32 AF XY: 0.144 AC XY: 10695 AN XY: 74368

African (AFR) AF: 0.113 AC: 4695 AN: 41524

American (AMR) AF: 0.133 AC: 2027 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0804 AC: 279 AN: 3468

East Asian (EAS) AF: 0.0744 AC: 386 AN: 5186

South Asian (SAS) AF: 0.0827 AC: 399 AN: 4826

European-Finnish (FIN) AF: 0.222 AC: 2346 AN: 10558

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11134 AN: 68000

Other (OTH) AF: 0.140 AC: 296 AN: 2110

Alfa AF: 0.150 Hom.: 7462

Bravo AF: 0.132

Asia WGS AF: 0.108 AC: 373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.074
DANN	Benign	0.61
PhyloP100		-2.4
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs9947485; hg19: chr18-74892855;