rs214527

Variant names:

• chr6-18291119-A-C
• rs214527
• ENST00000790360.1:n.459+13246A>C

Your query was ambiguous. Multiple possible variants found:

• chr6-18291119-A-C
• chr6-18291119-A-T

Variant summary

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

The ENST00000790360.1(ENSG00000289097):​n.459+13246A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 152,004 control chromosomes in the GnomAD database, including 7,218 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 0.29 (7218 hom., cov: 32)
• Consequence: ENSG00000289097 ENST00000790360.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510
• Publications: 4 publications found

Genes affected

ENSG00000289097 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.436 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
ENSG00000289097	ENST00000790360.1	n.459+13246A>C		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43587 AN: 151886 Hom.: 7201 Cov.: 32

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.0753

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.287 AC: 43660 AN: 152004 Hom.: 7218 Cov.: 32 AF XY: 0.287 AC XY: 21363 AN XY: 74328

African (AFR) AF: 0.442 AC: 18293 AN: 41416

American (AMR) AF: 0.351 AC: 5353 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1036 AN: 3466

East Asian (EAS) AF: 0.0757 AC: 392 AN: 5178

South Asian (SAS) AF: 0.342 AC: 1647 AN: 4816

European-Finnish (FIN) AF: 0.197 AC: 2086 AN: 10586

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.203 AC: 13814 AN: 67970

Other (OTH) AF: 0.285 AC: 601 AN: 2108

Alfa AF: 0.112 Hom.: 186

Bravo AF: 0.303

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.3
DANN	Benign	0.58
PhyloP100		-0.051

Splicing

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

Other links and lift over

dbSNP: rs214527; hg19: chr6-18291350;