rs1568483

chr6-140757642-G-C

Variant summary

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

The ENST00000650553.2(ENSG00000234147):n.293+58490C>G 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 0.43 in 152,000 control chromosomes in the GnomAD database, including 15,791 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 0.43 (15791 hom., cov: 32)
• Consequence: ENST00000650553.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920

Genes affected

(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 = 0.653 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378027	XR_001744387.3	n.1307-253G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000650553.2	n.293+58490C>G		intron_variant, non_coding_transcript_variant
	ENST00000684511.1	n.595-253G>C		intron_variant, non_coding_transcript_variant
	ENST00000682976.1	n.327-253G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65316 AN: 151882 Hom.: 15751 Cov.: 32

Gnomad AFR AF: 0.660

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.430 AC: 65412 AN: 152000 Hom.: 15791 Cov.: 32 AF XY: 0.426 AC XY: 31633 AN XY: 74278

Gnomad4 AFR AF: 0.660

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.399

Gnomad4 FIN AF: 0.347

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.414

Alfa AF: 0.380 Hom.: 1558

Bravo AF: 0.442

Asia WGS AF: 0.426 AC: 1485 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	0.58
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1568483; hg19: chr6-141078779; COSMIC: COSV68356889;