rs1402509

Variant names:

• chr6-140793927-C-T
• rs1402509
• ENST00000650553.2:n.293+22205G>A

Variant summary

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

The ENST00000650553.2(ENSG00000234147):​n.293+22205G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 151,892 control chromosomes in the GnomAD database, including 19,120 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 0.48 (19120 hom., cov: 32)
• Consequence: ENSG00000234147 ENST00000650553.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.380
• Publications: 1 publications found

Genes affected

ENSG00000234147 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.708 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650553.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000234147	ENST00000650553.2		n.293+22205G>A		intron	N/A
	ENSG00000234147	ENST00000826254.1		n.623+10308G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.477 AC: 72409 AN: 151772 Hom.: 19071 Cov.: 32

Gnomad AFR AF: 0.715

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.465

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

GnomAD4 genome AF: 0.477 AC: 72522 AN: 151892 Hom.: 19120 Cov.: 32 AF XY: 0.473 AC XY: 35095 AN XY: 74220

African (AFR) AF: 0.715 AC: 29636 AN: 41460

American (AMR) AF: 0.388 AC: 5919 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1290 AN: 3466

East Asian (EAS) AF: 0.330 AC: 1704 AN: 5158

South Asian (SAS) AF: 0.419 AC: 2016 AN: 4816

European-Finnish (FIN) AF: 0.390 AC: 4095 AN: 10502

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.387 AC: 26315 AN: 67928

Other (OTH) AF: 0.471 AC: 990 AN: 2104

Alfa AF: 0.410 Hom.: 6853

Bravo AF: 0.490

Asia WGS AF: 0.437 AC: 1513 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	1.5
DANN	Benign	0.87
PhyloP100		-0.38

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1402509;

hg19: chr6-141115064;