rs9943849

Variant names:

• chr12-68976976-C-T
• rs9943849
• ENST00000842813.1:n.103-6379C>T

Variant summary

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

The ENST00000842813.1(ENSG00000309659):​n.103-6379C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 152,114 control chromosomes in the GnomAD database, including 5,453 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 0.26 (5453 hom., cov: 32)
• Consequence: ENSG00000309659 ENST00000842813.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.544
• Publications: 13 publications found

Genes affected

ENSG00000309659 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.315 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
ENSG00000309659	ENST00000842813.1	n.103-6379C>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39866 AN: 151996 Hom.: 5442 Cov.: 32

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.262 AC: 39918 AN: 152114 Hom.: 5453 Cov.: 32 AF XY: 0.260 AC XY: 19370 AN XY: 74362

African (AFR) AF: 0.320 AC: 13263 AN: 41492

American (AMR) AF: 0.198 AC: 3024 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 1201 AN: 3470

East Asian (EAS) AF: 0.202 AC: 1047 AN: 5174

South Asian (SAS) AF: 0.288 AC: 1392 AN: 4828

European-Finnish (FIN) AF: 0.249 AC: 2637 AN: 10578

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.241 AC: 16412 AN: 67982

Other (OTH) AF: 0.241 AC: 508 AN: 2108

Alfa AF: 0.246 Hom.: 19557

Bravo AF: 0.260

Asia WGS AF: 0.284 AC: 985 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.94
DANN	Benign	0.73
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs9943849; hg19: chr12-69370756;