rs6789987

Variant names:

• chr3-188045610-C-T
• rs6789987
• ENST00000754169.1:n.177+8701C>T

Variant summary

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

The ENST00000754169.1(ENSG00000298263):​n.177+8701C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 151,872 control chromosomes in the GnomAD database, including 7,786 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 0.31 (7786 hom., cov: 31)
• Consequence: ENSG00000298263 ENST00000754169.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.251
• Publications: 8 publications found

Genes affected

ENSG00000298263 (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 = 0.443 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
ENSG00000298263	ENST00000754169.1	n.177+8701C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46408 AN: 151752 Hom.: 7770 Cov.: 31

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.306 AC: 46459 AN: 151872 Hom.: 7786 Cov.: 31 AF XY: 0.301 AC XY: 22365 AN XY: 74234

African (AFR) AF: 0.449 AC: 18574 AN: 41390

American (AMR) AF: 0.195 AC: 2968 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 993 AN: 3468

East Asian (EAS) AF: 0.136 AC: 703 AN: 5158

South Asian (SAS) AF: 0.146 AC: 702 AN: 4812

European-Finnish (FIN) AF: 0.319 AC: 3358 AN: 10534

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.269 AC: 18268 AN: 67940

Other (OTH) AF: 0.281 AC: 593 AN: 2112

Alfa AF: 0.275 Hom.: 17084

Bravo AF: 0.306

Asia WGS AF: 0.141 AC: 490 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	0.33
DANN	Benign	0.48
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs6789987; hg19: chr3-187763398;