rs262467

Variant names:

• chr6-120134624-T-C
• rs262467
• ENST00000834274.1:n.169+5983T>C

Variant summary

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

The ENST00000834274.1(ENSG00000308468):​n.169+5983T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 151,930 control chromosomes in the GnomAD database, including 14,899 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 0.42 (14899 hom., cov: 31)
• Consequence: ENSG00000308468 ENST00000834274.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.247
• Publications: 3 publications found

Genes affected

ENSG00000308468 (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 (EAS) allele frequency at 95% confidence interval = 0.572 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
ENSG00000308468	ENST00000834274.1	n.169+5983T>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63916 AN: 151810 Hom.: 14900 Cov.: 31

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.421 AC: 63940 AN: 151930 Hom.: 14899 Cov.: 31 AF XY: 0.428 AC XY: 31816 AN XY: 74262

African (AFR) AF: 0.207 AC: 8594 AN: 41468

American (AMR) AF: 0.468 AC: 7127 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1713 AN: 3468

East Asian (EAS) AF: 0.590 AC: 3041 AN: 5158

South Asian (SAS) AF: 0.548 AC: 2636 AN: 4814

European-Finnish (FIN) AF: 0.595 AC: 6263 AN: 10528

Middle Eastern (MID) AF: 0.435 AC: 127 AN: 292

European-Non Finnish (NFE) AF: 0.490 AC: 33286 AN: 67936

Other (OTH) AF: 0.434 AC: 918 AN: 2116

Alfa AF: 0.427 Hom.: 1860

Bravo AF: 0.405

Asia WGS AF: 0.564 AC: 1958 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.6
DANN	Benign	0.65
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs262467; hg19: chr6-120455770;