rs459162

Variant names:

• chr6-1216141-G-A
• rs459162
• ENST00000700915.2:n.230+12250C>T

Variant summary

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

The ENST00000700915.2(ENSG00000289842):​n.230+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 ENST00000700915.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200
• Publications: 4 publications found

Genes affected

ENSG00000289842 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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	ENST00000700915.2	n.230+12250C>T		intron_variant	Intron 1 of 2
ENSG00000289842	ENST00000702015.1	n.218+12250C>T		intron_variant	Intron 1 of 2
ENSG00000289842	ENST00000837382.1	n.111+12435C>T		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.549 AC: 22767 AN: 41452

American (AMR) AF: 0.419 AC: 6400 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 896 AN: 3472

East Asian (EAS) AF: 0.247 AC: 1271 AN: 5148

South Asian (SAS) AF: 0.366 AC: 1760 AN: 4812

European-Finnish (FIN) AF: 0.372 AC: 3930 AN: 10556

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.332 AC: 22596 AN: 67978

Other (OTH) AF: 0.398 AC: 836 AN: 2102

Alfa AF: 0.350 Hom.: 42126

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
PhyloP100		0.0020

Splicing

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

Other links and lift over

dbSNP: rs459162; hg19: chr6-1216376;