rs1343391

Variant names:

• chr6-58017876-C-G
• rs1343391
• ENST00000641775.1:n.172-9796C>G

Variant summary

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

The ENST00000641775.1(ENSG00000225096):​n.172-9796C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 151,926 control chromosomes in the GnomAD database, including 13,108 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 0.40 (13108 hom., cov: 31)
• Consequence: ENSG00000225096 ENST00000641775.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.387
• Publications: 4 publications found

Genes affected

ENSG00000225096 (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 = 0.566 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
ENSG00000225096	ENST00000641775.1	n.172-9796C>G		intron_variant	Intron 1 of 5
ENSG00000225096	ENST00000641829.1	n.444-9796C>G		intron_variant	Intron 4 of 7
ENSG00000225096	ENST00000666847.1	n.125-9796C>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60840 AN: 151808 Hom.: 13107 Cov.: 31

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.401 AC: 60863 AN: 151926 Hom.: 13108 Cov.: 31 AF XY: 0.408 AC XY: 30317 AN XY: 74264

African (AFR) AF: 0.263 AC: 10889 AN: 41430

American (AMR) AF: 0.559 AC: 8530 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1331 AN: 3466

East Asian (EAS) AF: 0.584 AC: 3003 AN: 5146

South Asian (SAS) AF: 0.554 AC: 2668 AN: 4820

European-Finnish (FIN) AF: 0.450 AC: 4747 AN: 10542

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.417 AC: 28351 AN: 67944

Other (OTH) AF: 0.423 AC: 891 AN: 2108

Alfa AF: 0.412 Hom.: 1697

Bravo AF: 0.400

Asia WGS AF: 0.461 AC: 1601 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.64
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs1343391; hg19: chr6-58344154;