rs7235543

Variant names:

• chr18-50992021-T-C
• rs7235543
• ENST00000590722.2:n.157+17460T>C

Variant summary

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

The ENST00000590722.2(ENSG00000267699):​n.157+17460T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0316 in 152,254 control chromosomes in the GnomAD database, including 173 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 0.032 (173 hom., cov: 32)
• Consequence: ENSG00000267699 ENST00000590722.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.111

Genes affected

ENSG00000267699 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0811 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985152	XR_001753449.3	n.6772A>G		non_coding_transcript_exon_variant	Exon 1 of 3
LOC107985152	XR_002958225.2	n.7178A>G		non_coding_transcript_exon_variant	Exon 1 of 4
LOC107985152	XR_007066371.1	n.7178A>G		non_coding_transcript_exon_variant	Exon 1 of 3
LOC107985152	XR_007066370.1	n.178-7681A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000267699	ENST00000590722.2	n.157+17460T>C		intron_variant	Intron 2 of 8	2		ENSP00000465737.1
ENSG00000267699	ENST00000588256.1	n.334+7458T>C		intron_variant	Intron 3 of 3	4

Frequencies

GnomAD3 genomes AF: 0.0315 AC: 4791 AN: 152136 Hom.: 173 Cov.: 32

Gnomad AFR AF: 0.0834

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0130

Gnomad ASJ AF: 0.0187

Gnomad EAS AF: 0.00481

Gnomad SAS AF: 0.0114

Gnomad FIN AF: 0.00443

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0128

Gnomad OTH AF: 0.0326

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

GnomAD4 genome AF: 0.0316 AC: 4804 AN: 152254 Hom.: 173 Cov.: 32 AF XY: 0.0310 AC XY: 2306 AN XY: 74456

Gnomad4 AFR AF: 0.0835

Gnomad4 AMR AF: 0.0129

Gnomad4 ASJ AF: 0.0187

Gnomad4 EAS AF: 0.00482

Gnomad4 SAS AF: 0.0116

Gnomad4 FIN AF: 0.00443

Gnomad4 NFE AF: 0.0128

Gnomad4 OTH AF: 0.0318

Alfa AF: 0.0228 Hom.: 16

Bravo AF: 0.0343

Asia WGS AF: 0.0150 AC: 53 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	12
DANN	Benign	0.68

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7235543; hg19: chr18-48518391;