rs700131

Variant names:

• chr9-111214463-T-C
• rs700131
• ENST00000426204.1:n.370+58350A>G

Variant summary

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

The ENST00000426204.1(ENSG00000227531):​n.370+58350A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 152,086 control chromosomes in the GnomAD database, including 3,938 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 0.21 (3938 hom., cov: 32)
• Consequence: ENSG00000227531 ENST00000426204.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 1 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=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.279 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+58350A>G		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32583 AN: 151968 Hom.: 3935 Cov.: 32

Gnomad AFR AF: 0.0984

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.214 AC: 32610 AN: 152086 Hom.: 3938 Cov.: 32 AF XY: 0.212 AC XY: 15752 AN XY: 74356

African (AFR) AF: 0.0985 AC: 4089 AN: 41528

American (AMR) AF: 0.205 AC: 3133 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 843 AN: 3466

East Asian (EAS) AF: 0.204 AC: 1056 AN: 5172

South Asian (SAS) AF: 0.291 AC: 1404 AN: 4818

European-Finnish (FIN) AF: 0.224 AC: 2368 AN: 10574

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.278 AC: 18891 AN: 67942

Other (OTH) AF: 0.232 AC: 490 AN: 2112

Alfa AF: 0.250 Hom.: 13517

Bravo AF: 0.205

Asia WGS AF: 0.277 AC: 960 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.7
DANN	Benign	0.70
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs700131; hg19: chr9-113976743;