chr6-43858890-C-T

Variant names:

• chr6-43858890-C-T
• rs943080
• ENST00000719551.1:n.315+16257C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000719551.1(ENSG00000283573):​n.315+16257C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.609 in 152,044 control chromosomes in the GnomAD database, including 29,476 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).

• Frequency: Genomes: 𝑓 0.61 (29476 hom., cov: 32)
• Consequence: ENSG00000283573 ENST00000719551.1 intron
• Clinical Significance: not provided no classification provided O:1
• Conservation: PhyloP100: 0.773
• Publications: 81 publications found

Genes affected

ENSG00000283573 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375070	XR_007059588.1	n.315+16257C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283573	ENST00000719551.1	n.315+16257C>T		intron_variant	Intron 2 of 2
ENSG00000283573	ENST00000719552.1	n.403+16257C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.609 AC: 92553 AN: 151926 Hom.: 29428 Cov.: 32

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.609 AC: 92661 AN: 152044 Hom.: 29476 Cov.: 32 AF XY: 0.615 AC XY: 45731 AN XY: 74320

African (AFR) AF: 0.801 AC: 33226 AN: 41494

American (AMR) AF: 0.545 AC: 8323 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1806 AN: 3470

East Asian (EAS) AF: 0.729 AC: 3764 AN: 5162

South Asian (SAS) AF: 0.653 AC: 3151 AN: 4822

European-Finnish (FIN) AF: 0.582 AC: 6142 AN: 10556

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.506 AC: 34375 AN: 67948

Other (OTH) AF: 0.604 AC: 1275 AN: 2110

Alfa AF: 0.541 Hom.: 97668

Bravo AF: 0.612

Asia WGS AF: 0.684 AC: 2376 AN: 3478

ClinVar

Significance: not provided

Submissions summary: Other:1

Revision: no classification provided

Submissions by phenotype

not provided Other:1

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Department of Ophthalmology and Visual Sciences Kyoto University

Significance: not provided

Review Status: no classification provided

Collection Method: not provided

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	14
DANN	Benign	0.67
PhyloP100		0.77

Splicing

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

Other links and lift over

dbSNP: rs943080; hg19: chr6-43826627;