rs1568483

Variant names:

• chr6-140757642-G-C
• rs1568483
• ENST00000650553.2:n.293+58490C>G

Variant summary

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

The ENST00000650553.2(ENSG00000234147):​n.293+58490C>G variant causes a intron 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: ENSG00000234147 ENST00000650553.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920
• Publications: 0 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.653 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+58490C>G		intron	N/A
	ENSG00000288714	ENST00000682976.1		n.327-253G>C		intron	N/A
	ENSG00000288714	ENST00000684511.1		n.595-253G>C		intron	N/A

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

African (AFR) AF: 0.660 AC: 27356 AN: 41464

American (AMR) AF: 0.337 AC: 5137 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1176 AN: 3464

East Asian (EAS) AF: 0.331 AC: 1707 AN: 5162

South Asian (SAS) AF: 0.399 AC: 1920 AN: 4816

European-Finnish (FIN) AF: 0.347 AC: 3660 AN: 10534

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.339 AC: 23080 AN: 67988

Other (OTH) AF: 0.414 AC: 872 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.58
DANN	Benign	0.40
PhyloP100		-0.092

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: rs1568483;

hg19: chr6-141078779;

COSMIC: COSV68356889;