rs4131672

Variant names:

• chr18-77540028-G-C
• rs4131672
• ENST00000583629.2:n.497+17106G>C

Variant summary

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

The ENST00000583629.2(ENSG00000264015):​n.497+17106G>C variant causes a intron 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: ENSG00000264015 ENST00000583629.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.305
• Publications: 2 publications found

Genes affected

ENSG00000264015 (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 = 0.443 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985172	XR_001753512.2	n.478+17106G>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000264015	ENST00000583629.2	n.497+17106G>C		intron_variant	Intron 2 of 2	4
ENSG00000264015	ENST00000744289.1	n.270+17106G>C		intron_variant	Intron 3 of 3
ENSG00000264015	ENST00000744290.1	n.496-73155G>C		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.448 AC: 18550 AN: 41406

American (AMR) AF: 0.306 AC: 4669 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 465 AN: 3470

East Asian (EAS) AF: 0.0633 AC: 328 AN: 5178

South Asian (SAS) AF: 0.144 AC: 693 AN: 4826

European-Finnish (FIN) AF: 0.0879 AC: 930 AN: 10578

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.192 AC: 13028 AN: 67982

Other (OTH) AF: 0.236 AC: 498 AN: 2110

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
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs4131672; hg19: chr18-75251984;