chr3-191064734-C-T

Variant names:

• chr3-191064734-C-T
• rs2048417
• ENST00000843941.1:n.147-23405C>T

Variant summary

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

The ENST00000843941.1(ENSG00000309795):​n.147-23405C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 151,536 control chromosomes in the GnomAD database, including 22,401 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 (22401 hom., cov: 32)
• Consequence: ENSG00000309795 ENST00000843941.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.285
• Publications: 5 publications found

Genes affected

ENSG00000309795 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.728 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
ENSG00000309795	ENST00000843941.1	n.147-23405C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.526 AC: 79676 AN: 151428 Hom.: 22359 Cov.: 32

Gnomad AFR AF: 0.735

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.526 AC: 79764 AN: 151536 Hom.: 22401 Cov.: 32 AF XY: 0.522 AC XY: 38614 AN XY: 73970

African (AFR) AF: 0.735 AC: 30403 AN: 41368

American (AMR) AF: 0.462 AC: 7034 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.489 AC: 1696 AN: 3468

East Asian (EAS) AF: 0.462 AC: 2373 AN: 5140

South Asian (SAS) AF: 0.331 AC: 1590 AN: 4810

European-Finnish (FIN) AF: 0.394 AC: 4096 AN: 10388

Middle Eastern (MID) AF: 0.503 AC: 144 AN: 286

European-Non Finnish (NFE) AF: 0.455 AC: 30847 AN: 67858

Other (OTH) AF: 0.515 AC: 1077 AN: 2092

Alfa AF: 0.468 Hom.: 23500

Bravo AF: 0.546

Asia WGS AF: 0.379 AC: 1312 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.33
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs2048417; hg19: chr3-190782523;