rs199131

Variant names:

• chr6-23557933-G-A
• rs199131
• ENST00000690652.3:n.355+26171C>T

Variant summary

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

The ENST00000690652.3(ENSG00000289368):​n.355+26171C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 151,948 control chromosomes in the GnomAD database, including 2,595 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 0.11 (2595 hom., cov: 31)
• Consequence: ENSG00000289368 ENST00000690652.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 1 publications found

Genes affected

ENSG00000289368 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374976	XR_001744046.2	n.400+48010C>T		intron_variant	Intron 3 of 6
LOC105374976	XR_007059501.1	n.378+48010C>T		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289368	ENST00000690652.3	n.355+26171C>T		intron_variant	Intron 1 of 2
ENSG00000289368	ENST00000700866.2	n.180+26171C>T		intron_variant	Intron 1 of 2
ENSG00000289368	ENST00000700904.2	n.201-12576C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17119 AN: 151830 Hom.: 2586 Cov.: 31

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0618

Gnomad ASJ AF: 0.0144

Gnomad EAS AF: 0.00387

Gnomad SAS AF: 0.0185

Gnomad FIN AF: 0.00623

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0199

Gnomad OTH AF: 0.0887

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

GnomAD4 genome AF: 0.113 AC: 17172 AN: 151948 Hom.: 2595 Cov.: 31 AF XY: 0.110 AC XY: 8166 AN XY: 74288

African (AFR) AF: 0.349 AC: 14428 AN: 41396

American (AMR) AF: 0.0615 AC: 939 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0144 AC: 50 AN: 3466

East Asian (EAS) AF: 0.00388 AC: 20 AN: 5152

South Asian (SAS) AF: 0.0181 AC: 87 AN: 4808

European-Finnish (FIN) AF: 0.00623 AC: 66 AN: 10590

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0199 AC: 1352 AN: 67964

Other (OTH) AF: 0.0878 AC: 185 AN: 2108

Alfa AF: 0.0709 Hom.: 188

Bravo AF: 0.127

Asia WGS AF: 0.0330 AC: 115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.71
DANN	Benign	0.34
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs199131; hg19: chr6-23558161;