4-180511711-C-T

Variant names:

• chr4-180511711-C-T
• rs2546613
• ENST00000761151.1:n.216-27960C>T

Variant summary

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

The ENST00000761151.1(ENSG00000299149):​n.216-27960C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 151,948 control chromosomes in the GnomAD database, including 26,378 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 0.59 (26378 hom., cov: 32)
• Consequence: ENSG00000299149 ENST00000761151.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.880
• Publications: 1 publications found

Genes affected

ENSG00000299149 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000761151.1. 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
	ENSG00000299149	ENST00000761151.1		n.216-27960C>T		intron	N/A
	ENSG00000289951	ENST00000761354.1		n.185+16425G>A		intron	N/A
	ENSG00000289951	ENST00000761355.1		n.225+16425G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88854 AN: 151830 Hom.: 26353 Cov.: 32

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.585 AC: 88921 AN: 151948 Hom.: 26378 Cov.: 32 AF XY: 0.589 AC XY: 43752 AN XY: 74284

African (AFR) AF: 0.490 AC: 20278 AN: 41418

American (AMR) AF: 0.672 AC: 10254 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1908 AN: 3464

East Asian (EAS) AF: 0.537 AC: 2771 AN: 5158

South Asian (SAS) AF: 0.656 AC: 3162 AN: 4822

European-Finnish (FIN) AF: 0.636 AC: 6712 AN: 10558

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.615 AC: 41800 AN: 67950

Other (OTH) AF: 0.581 AC: 1224 AN: 2108

Alfa AF: 0.598 Hom.: 3296

Bravo AF: 0.579

Asia WGS AF: 0.591 AC: 2053 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.34
DANN	Benign	0.26
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs2546613; hg19: chr4-181432864;