chr6-140757642-G-C

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378027	XR_001744385.2	n.1307-253G>C		intron_variant	Intron 4 of 8
LOC105378027	XR_001744387.3	n.1307-253G>C		intron_variant	Intron 4 of 7
LOC105378027	XR_001744388.2	n.1209-253G>C		intron_variant	Intron 3 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234147	ENST00000650553.2	n.293+58490C>G		intron_variant	Intron 2 of 4
ENSG00000288714	ENST00000682976.1	n.327-253G>C		intron_variant	Intron 2 of 2
ENSG00000288714	ENST00000684511.1	n.595-253G>C		intron_variant	Intron 5 of 8

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 v4.3

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

Other links and lift over

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