rs13191099

Variant names:

• chr6-31273225-A-G
• rs13191099
• ENST00000755297.1:n.32+2119A>G

Variant summary

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

The ENST00000755297.1(ENSG00000298396):​n.32+2119A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 150,574 control chromosomes in the GnomAD database, including 1,624 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 0.14 (1624 hom., cov: 32)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.234
• Publications: 9 publications found

Genes affected

ENSG00000298396 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298396	ENST00000755297.1	n.32+2119A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20724 AN: 150458 Hom.: 1623 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.138 AC: 20725 AN: 150574 Hom.: 1624 Cov.: 32 AF XY: 0.139 AC XY: 10268 AN XY: 73612

African (AFR) AF: 0.111 AC: 4448 AN: 40178

American (AMR) AF: 0.122 AC: 1839 AN: 15100

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 1274 AN: 3470

East Asian (EAS) AF: 0.108 AC: 560 AN: 5190

South Asian (SAS) AF: 0.256 AC: 1234 AN: 4812

European-Finnish (FIN) AF: 0.100 AC: 1060 AN: 10568

Middle Eastern (MID) AF: 0.267 AC: 77 AN: 288

European-Non Finnish (NFE) AF: 0.143 AC: 9711 AN: 67970

Other (OTH) AF: 0.153 AC: 319 AN: 2086

Alfa AF: 0.129 Hom.: 220

Bravo AF: 0.134

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	9.8
DANN	Benign	0.49
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs13191099; hg19: chr6-31241002;