6-43858890-C-T

Variant names:

• chr6-43858890-C-T
• rs943080
• XR_007059588.1:n.315+16257C>T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_007059588.1(LOC105375070):​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: LOC105375070 XR_007059588.1 intron
• Clinical Significance: not provided no classification provided O:1
• Conservation: PhyloP100: 0.773

Genes affected

LOC105375070 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.801

Gnomad4 AMR AF: 0.545

Gnomad4 ASJ AF: 0.520

Gnomad4 EAS AF: 0.729

Gnomad4 SAS AF: 0.653

Gnomad4 FIN AF: 0.582

Gnomad4 NFE AF: 0.506

Gnomad4 OTH AF: 0.604

Alfa AF: 0.529 Hom.: 44389

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs943080; hg19: chr6-43826627;