3-196591984-C-T

Variant names:

• chr3-196591984-C-T
• rs9843585
• ENST00000726919.1:n.379+1143C>T

Variant summary

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

The ENST00000726919.1(ENSG00000294939):​n.379+1143C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.624 in 150,580 control chromosomes in the GnomAD database, including 29,433 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 0.62 (29433 hom., cov: 27)
• Consequence: ENSG00000294939 ENST00000726919.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.782
• Publications: 4 publications found

Genes affected

ENSG00000294939 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.713 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
ENSG00000294939	ENST00000726919.1	n.379+1143C>T		intron_variant	Intron 1 of 1
ENSG00000294939	ENST00000726920.1	n.371+1119C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.624 AC: 93862 AN: 150482 Hom.: 29401 Cov.: 27

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.680

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.644

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.624 AC: 93937 AN: 150580 Hom.: 29433 Cov.: 27 AF XY: 0.627 AC XY: 46123 AN XY: 73572

African (AFR) AF: 0.555 AC: 22549 AN: 40632

American (AMR) AF: 0.621 AC: 9430 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2188 AN: 3464

East Asian (EAS) AF: 0.681 AC: 3472 AN: 5100

South Asian (SAS) AF: 0.733 AC: 3512 AN: 4792

European-Finnish (FIN) AF: 0.690 AC: 7157 AN: 10370

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.644 AC: 43656 AN: 67760

Other (OTH) AF: 0.607 AC: 1261 AN: 2078

Alfa AF: 0.634 Hom.: 52847

Bravo AF: 0.612

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.21
DANN	Benign	0.65
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs9843585; hg19: chr3-196318855;