chr4-11546343-C-A

Variant names:

• chr4-11546343-C-A
• rs756418
• ENST00000790104.1:n.303+2180C>A

Variant summary

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

The NR_188483.1(LOC107986178):​n.191+2180C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0989 in 152,250 control chromosomes in the GnomAD database, including 942 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 0.099 (942 hom., cov: 32)
• Consequence: LOC107986178 NR_188483.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.591
• Publications: 3 publications found

Genes affected

ENSG00000302860 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_188483.1. 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
	LOC107986178	NR_188483.1		n.191+2180C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302860	ENST00000790104.1		n.303+2180C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0989 AC: 15050 AN: 152132 Hom.: 944 Cov.: 32

Gnomad AFR AF: 0.0292

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.0588

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.0989 AC: 15052 AN: 152250 Hom.: 942 Cov.: 32 AF XY: 0.0988 AC XY: 7351 AN XY: 74438

African (AFR) AF: 0.0292 AC: 1212 AN: 41564

American (AMR) AF: 0.190 AC: 2902 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 479 AN: 3468

East Asian (EAS) AF: 0.105 AC: 542 AN: 5170

South Asian (SAS) AF: 0.148 AC: 715 AN: 4826

European-Finnish (FIN) AF: 0.0588 AC: 623 AN: 10600

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8244 AN: 68016

Other (OTH) AF: 0.106 AC: 224 AN: 2110

Alfa AF: 0.121 Hom.: 1849

Bravo AF: 0.105

Asia WGS AF: 0.118 AC: 412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.67
DANN	Benign	0.59
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs756418; hg19: chr4-11547967;