6-43860845-T-C

Variant names:

• chr6-43860845-T-C
• rs4711751
• ENST00000719551.1:n.315+18212T>C

Variant summary

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

The ENST00000719551.1(ENSG00000283573):​n.315+18212T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 152,186 control chromosomes in the GnomAD database, including 12,445 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 0.37 (12445 hom., cov: 34)
• Consequence: ENSG00000283573 ENST00000719551.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.741
• Publications: 37 publications found

Genes affected

ENSG00000283573 (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 (NFE) allele frequency at 95% confidence interval = 0.491 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+18212T>C		intron	N/A
	ENSG00000283573	ENST00000719552.1		n.403+18212T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56467 AN: 152068 Hom.: 12446 Cov.: 34

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.371 AC: 56469 AN: 152186 Hom.: 12445 Cov.: 34 AF XY: 0.366 AC XY: 27240 AN XY: 74410

African (AFR) AF: 0.127 AC: 5284 AN: 41540

American (AMR) AF: 0.449 AC: 6867 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1657 AN: 3468

East Asian (EAS) AF: 0.271 AC: 1404 AN: 5180

South Asian (SAS) AF: 0.346 AC: 1670 AN: 4828

European-Finnish (FIN) AF: 0.426 AC: 4506 AN: 10582

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.495 AC: 33675 AN: 67988

Other (OTH) AF: 0.382 AC: 807 AN: 2110

Alfa AF: 0.435 Hom.: 25218

Bravo AF: 0.365

Asia WGS AF: 0.314 AC: 1094 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.24
DANN	Benign	0.48
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs4711751; hg19: chr6-43828582;