rs10980800

Variant names:

• chr9-111153625-T-C
• rs10980800
• ENST00000426204.1:n.371-14006A>G

Variant summary

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

The ENST00000426204.1(ENSG00000227531):​n.371-14006A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,102 control chromosomes in the GnomAD database, including 3,449 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 (3449 hom., cov: 32)
• Consequence: ENSG00000227531 ENST00000426204.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270

Genes affected

ENSG00000227531 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.224 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.371-14006A>G		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32024 AN: 151984 Hom.: 3448 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.0803

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.211 AC: 32036 AN: 152102 Hom.: 3449 Cov.: 32 AF XY: 0.208 AC XY: 15472 AN XY: 74364

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.0800

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.227

Gnomad4 OTH AF: 0.219

Alfa AF: 0.223 Hom.: 6515

Bravo AF: 0.209

Asia WGS AF: 0.114 AC: 399 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	9.5
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10980800; hg19: chr9-113915905;