rs459162

Variant names:

• chr6-1216141-G-A
• rs459162
• ENST00000700915.1:n.218+12250C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000700915.1(ENSG00000289842):​n.218+12250C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 152,010 control chromosomes in the GnomAD database, including 13,045 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 0.40 (13045 hom., cov: 32)
• Consequence: ENSG00000289842 ENST00000700915.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200

Genes affected

ENSG00000289842 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.543 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
ENSG00000289842	ENST00000700915.1	n.218+12250C>T		intron_variant	Intron 1 of 2
ENSG00000289842	ENST00000702015.1	n.218+12250C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60780 AN: 151892 Hom.: 13009 Cov.: 32

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.400 AC: 60872 AN: 152010 Hom.: 13045 Cov.: 32 AF XY: 0.402 AC XY: 29890 AN XY: 74308

Gnomad4 AFR AF: 0.549

Gnomad4 AMR AF: 0.419

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.247

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.372

Gnomad4 NFE AF: 0.332

Gnomad4 OTH AF: 0.398

Alfa AF: 0.339 Hom.: 18708

Bravo AF: 0.408

Asia WGS AF: 0.339 AC: 1180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.5
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs459162; hg19: chr6-1216376;