rs4943543

Variant names:

• chr13-37900250-G-A
• rs4943543
• ENST00000838014.1:n.126-18163C>T

Your query was ambiguous. Multiple possible variants found:

• chr13-37900250-G-A
• chr13-37900250-G-C
• chr13-37900250-G-T

Variant summary

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

The ENST00000838014.1(ENSG00000309047):​n.126-18163C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 151,996 control chromosomes in the GnomAD database, including 6,747 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 0.28 (6747 hom., cov: 32)
• Consequence: ENSG00000309047 ENST00000838014.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 5 publications found

Genes affected

ENSG00000309047 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000838014.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309047	ENST00000838014.1		n.126-18163C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43279 AN: 151878 Hom.: 6735 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.285 AC: 43317 AN: 151996 Hom.: 6747 Cov.: 32 AF XY: 0.290 AC XY: 21576 AN XY: 74300

African (AFR) AF: 0.211 AC: 8761 AN: 41462

American (AMR) AF: 0.308 AC: 4695 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1008 AN: 3470

East Asian (EAS) AF: 0.591 AC: 3044 AN: 5152

South Asian (SAS) AF: 0.392 AC: 1892 AN: 4826

European-Finnish (FIN) AF: 0.355 AC: 3755 AN: 10564

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.284 AC: 19315 AN: 67944

Other (OTH) AF: 0.277 AC: 585 AN: 2110

Alfa AF: 0.274 Hom.: 16494

Bravo AF: 0.276

Asia WGS AF: 0.488 AC: 1694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.47
DANN	Benign	0.46
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs4943543; hg19: chr13-38474387;