rs4131672

chr18-77540028-G-C

Variant summary

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

The ENST00000583629.2(ENSG00000264015):n.497+17106G>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 0.259 in 152,028 control chromosomes in the GnomAD database, including 6,396 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 0.26 (6396 hom., cov: 32)
• Consequence: ENST00000583629.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.305

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 = 0.443 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985172	XR_001753512.2	n.478+17106G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000583629.2	n.497+17106G>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39311 AN: 151908 Hom.: 6388 Cov.: 32

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.0632

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.0879

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.259 AC: 39356 AN: 152028 Hom.: 6396 Cov.: 32 AF XY: 0.250 AC XY: 18557 AN XY: 74344

Gnomad4 AFR AF: 0.448

Gnomad4 AMR AF: 0.306

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.0633

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.0879

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.236

Alfa AF: 0.231 Hom.: 628

Bravo AF: 0.287

Asia WGS AF: 0.150 AC: 523 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	0.87
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4131672; hg19: chr18-75251984;