6-43858890-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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000719551.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000283573	ENST00000719551.1		n.315+16257C>T		intron	N/A
	ENSG00000283573	ENST00000719552.1		n.403+16257C>T		intron	N/A

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

ClinVar submissions

Significance: not provided

Revision: no classification provided

Pathogenic	VUS	Benign	Condition
-	-	-	not provided (1)

Computational scores

Source: dbNSFP v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs943080;

hg19: chr6-43826627;