rs87939

Variant names:

• chr3-41096353-G-A
• rs87939
• ENST00000808368.1:n.394+197C>T

Variant summary

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

The ENST00000808368.1(ENSG00000305067):​n.394+197C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 152,018 control chromosomes in the GnomAD database, including 16,088 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 0.44 (16088 hom., cov: 32)
• Consequence: ENSG00000305067 ENST00000808368.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.583
• Publications: 5 publications found

Genes affected

ENSG00000305067 (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 = 0.546 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000808368.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305067	ENST00000808368.1		n.394+197C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66604 AN: 151900 Hom.: 16081 Cov.: 32

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.438 AC: 66638 AN: 152018 Hom.: 16088 Cov.: 32 AF XY: 0.432 AC XY: 32131 AN XY: 74292

African (AFR) AF: 0.269 AC: 11164 AN: 41444

American (AMR) AF: 0.418 AC: 6378 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1432 AN: 3468

East Asian (EAS) AF: 0.244 AC: 1262 AN: 5174

South Asian (SAS) AF: 0.275 AC: 1326 AN: 4822

European-Finnish (FIN) AF: 0.583 AC: 6154 AN: 10556

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.550 AC: 37391 AN: 67962

Other (OTH) AF: 0.451 AC: 953 AN: 2112

Alfa AF: 0.452 Hom.: 4717

Bravo AF: 0.421

Asia WGS AF: 0.286 AC: 996 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0090
DANN	Benign	0.29
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs87939; hg19: chr3-41137844;