rs12186641

Variant names:

• chr5-51868281-C-T
• rs12186641
• ENST00000771174.1:n.918-6611G>A

Variant summary

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

The ENST00000771174.1(ENSG00000300361):​n.918-6611G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0567 in 151,902 control chromosomes in the GnomAD database, including 272 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 0.057 (272 hom., cov: 32)
• Consequence: ENSG00000300361 ENST00000771174.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.809
• Publications: 4 publications found

Genes affected

ENSG00000300361 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0722 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300361	ENST00000771174.1	n.918-6611G>A		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.0567 AC: 8603 AN: 151784 Hom.: 272 Cov.: 32

Gnomad AFR AF: 0.0429

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0528

Gnomad ASJ AF: 0.0569

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0303

Gnomad FIN AF: 0.0452

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0739

Gnomad OTH AF: 0.0713

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

GnomAD4 genome AF: 0.0567 AC: 8606 AN: 151902 Hom.: 272 Cov.: 32 AF XY: 0.0547 AC XY: 4063 AN XY: 74260

African (AFR) AF: 0.0428 AC: 1777 AN: 41480

American (AMR) AF: 0.0527 AC: 803 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.0569 AC: 197 AN: 3464

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5182

South Asian (SAS) AF: 0.0307 AC: 148 AN: 4816

European-Finnish (FIN) AF: 0.0452 AC: 479 AN: 10596

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0739 AC: 5011 AN: 67822

Other (OTH) AF: 0.0710 AC: 150 AN: 2112

Alfa AF: 0.0642 Hom.: 268

Bravo AF: 0.0568

Asia WGS AF: 0.0190 AC: 65 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	14
DANN	Benign	0.65
PhyloP100		0.81

Splicing

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

Other links and lift over

dbSNP: rs12186641; hg19: chr5-51164115;