rs700137

Variant names:

• chr9-111235509-A-G
• rs700137
• ENST00000426204.1:n.370+37304T>C

Variant summary

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

The ENST00000426204.1(ENSG00000227531):​n.370+37304T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 151,984 control chromosomes in the GnomAD database, including 3,747 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 0.20 (3747 hom., cov: 32)
• Consequence: ENSG00000227531 ENST00000426204.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.330
• Publications: 3 publications found

Genes affected

ENSG00000227531 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.275 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
ENSG00000227531	ENST00000426204.1	n.370+37304T>C		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31110 AN: 151866 Hom.: 3744 Cov.: 32

Gnomad AFR AF: 0.0775

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.205 AC: 31130 AN: 151984 Hom.: 3747 Cov.: 32 AF XY: 0.201 AC XY: 14939 AN XY: 74278

African (AFR) AF: 0.0773 AC: 3208 AN: 41498

American (AMR) AF: 0.191 AC: 2921 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 788 AN: 3470

East Asian (EAS) AF: 0.154 AC: 796 AN: 5170

South Asian (SAS) AF: 0.272 AC: 1310 AN: 4820

European-Finnish (FIN) AF: 0.227 AC: 2381 AN: 10510

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.279 AC: 18937 AN: 67934

Other (OTH) AF: 0.219 AC: 462 AN: 2112

Alfa AF: 0.253 Hom.: 5116

Bravo AF: 0.194

Asia WGS AF: 0.243 AC: 844 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.5
DANN	Benign	0.64
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs700137; hg19: chr9-113997789;