rs1321413

Variant names:

• chr20-61137005-C-T
• rs1321413
• ENST00000781103.1:n.291+8518G>A

Variant summary

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

The ENST00000781103.1(ENSG00000289577):​n.291+8518G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 152,060 control chromosomes in the GnomAD database, including 9,421 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 0.32 (9421 hom., cov: 32)
• Consequence: ENSG00000289577 ENST00000781103.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.425
• Publications: 3 publications found

Genes affected

ENSG00000289577 (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 = 0.44 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
ENSG00000289577	ENST00000781103.1	n.291+8518G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48579 AN: 151942 Hom.: 9422 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.319 AC: 48583 AN: 152060 Hom.: 9421 Cov.: 32 AF XY: 0.317 AC XY: 23555 AN XY: 74342

African (AFR) AF: 0.116 AC: 4818 AN: 41496

American (AMR) AF: 0.306 AC: 4668 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1227 AN: 3470

East Asian (EAS) AF: 0.129 AC: 667 AN: 5166

South Asian (SAS) AF: 0.217 AC: 1047 AN: 4830

European-Finnish (FIN) AF: 0.449 AC: 4746 AN: 10562

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.444 AC: 30153 AN: 67946

Other (OTH) AF: 0.329 AC: 694 AN: 2110

Alfa AF: 0.393 Hom.: 38317

Bravo AF: 0.303

Asia WGS AF: 0.162 AC: 565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.36
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs1321413; hg19: chr20-59712061;