rs4733724

chr8-129711482-A-G

Variant summary

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

The ENST00000646849.1(ENSG00000285108):n.48-4300T>C 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 0.4 in 152,086 control chromosomes in the GnomAD database, including 17,239 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 0.40 (17239 hom., cov: 32)
• Consequence: ENST00000646849.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GSDMC	XR_928339.3	n.2054-4300T>C		intron_variant, non_coding_transcript_variant
GSDMC	XR_928340.3	n.2054-4300T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000646849.1	n.48-4300T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60745 AN: 151968 Hom.: 17194 Cov.: 32

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.716

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.400 AC: 60854 AN: 152086 Hom.: 17239 Cov.: 32 AF XY: 0.402 AC XY: 29855 AN XY: 74354

Gnomad4 AFR AF: 0.772

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.716

Gnomad4 SAS AF: 0.433

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.377

Alfa AF: 0.243 Hom.: 6084

Bravo AF: 0.434

Asia WGS AF: 0.613 AC: 2130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.078
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4733724; hg19: chr8-130723728;