rs1402509

Positions:

• chr6-140793927-C-T

Variant summary

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

The ENST00000650553.2(ENSG00000234147):​n.293+22205G>A variant causes a intron, non coding transcript 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: ENST00000650553.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.380

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102723724	XR_428030.5	n.30867-109G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000650553.2	n.293+22205G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.715

Gnomad4 AMR AF: 0.388

Gnomad4 ASJ AF: 0.372

Gnomad4 EAS AF: 0.330

Gnomad4 SAS AF: 0.419

Gnomad4 FIN AF: 0.390

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.471

Alfa AF: 0.410 Hom.: 6211

Bravo AF: 0.490

Asia WGS AF: 0.437 AC: 1513 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1402509; hg19: chr6-141115064;