rs4878061

Variant names:

• chr9-87344686-G-A
• rs4878061
• ENST00000690842.2:n.742+40157C>T

Variant summary

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

The ENST00000690842.2(ENSG00000289166):​n.742+40157C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 152,054 control chromosomes in the GnomAD database, including 22,497 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 0.53 (22497 hom., cov: 32)
• Consequence: ENSG00000289166 ENST00000690842.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.764
• Publications: 2 publications found

Genes affected

ENSG00000289166 (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 (AFR) allele frequency at 95% confidence interval = 0.688 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
ENSG00000289166	ENST00000690842.2	n.742+40157C>T		intron_variant	Intron 2 of 4
ENSG00000289166	ENST00000804132.1	n.216+41879C>T		intron_variant	Intron 1 of 3
ENSG00000289166	ENST00000804133.1	n.378+40157C>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80455 AN: 151936 Hom.: 22465 Cov.: 32

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.530 AC: 80539 AN: 152054 Hom.: 22497 Cov.: 32 AF XY: 0.524 AC XY: 38929 AN XY: 74330

African (AFR) AF: 0.695 AC: 28832 AN: 41472

American (AMR) AF: 0.403 AC: 6153 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.415 AC: 1436 AN: 3464

East Asian (EAS) AF: 0.166 AC: 855 AN: 5162

South Asian (SAS) AF: 0.408 AC: 1966 AN: 4824

European-Finnish (FIN) AF: 0.557 AC: 5888 AN: 10570

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.499 AC: 33931 AN: 67970

Other (OTH) AF: 0.467 AC: 989 AN: 2116

Alfa AF: 0.506 Hom.: 9612

Bravo AF: 0.523

Asia WGS AF: 0.350 AC: 1218 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	0.23
DANN	Benign	0.62
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs4878061; hg19: chr9-89959601;