rs1341622

Variant names:

• chr13-54530436-G-A
• rs1341622
• ENST00000748854.1:n.173-2021C>T

Variant summary

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

The ENST00000748854.1(ENSG00000297549):​n.173-2021C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.842 in 152,032 control chromosomes in the GnomAD database, including 54,038 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 0.84 (54038 hom., cov: 31)
• Consequence: ENSG00000297549 ENST00000748854.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290
• Publications: 2 publications found

Genes affected

ENSG00000297549 (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 = 0.914 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
ENSG00000297549	ENST00000748854.1	n.173-2021C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.842 AC: 127863 AN: 151916 Hom.: 53982 Cov.: 31

Gnomad AFR AF: 0.921

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.783

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.852

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.827

Gnomad OTH AF: 0.834

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

GnomAD4 genome AF: 0.842 AC: 127980 AN: 152032 Hom.: 54038 Cov.: 31 AF XY: 0.836 AC XY: 62121 AN XY: 74300

African (AFR) AF: 0.921 AC: 38247 AN: 41508

American (AMR) AF: 0.783 AC: 11947 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.822 AC: 2853 AN: 3470

East Asian (EAS) AF: 0.742 AC: 3818 AN: 5146

South Asian (SAS) AF: 0.853 AC: 4105 AN: 4814

European-Finnish (FIN) AF: 0.750 AC: 7906 AN: 10536

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.827 AC: 56251 AN: 67986

Other (OTH) AF: 0.837 AC: 1769 AN: 2114

Alfa AF: 0.835 Hom.: 23359

Bravo AF: 0.843

Asia WGS AF: 0.829 AC: 2877 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.38
DANN	Benign	0.60
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs1341622; hg19: chr13-55104571;