rs10980800

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000426204.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000227531	ENST00000426204.1	TSL:3	n.371-14006A>G		intron	N/A

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

African (AFR) AF: 0.222 AC: 9200 AN: 41492

American (AMR) AF: 0.163 AC: 2492 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 737 AN: 3470

East Asian (EAS) AF: 0.0800 AC: 414 AN: 5178

South Asian (SAS) AF: 0.164 AC: 789 AN: 4822

European-Finnish (FIN) AF: 0.221 AC: 2330 AN: 10566

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.227 AC: 15409 AN: 67970

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

Alfa AF: 0.223 Hom.: 15242

Bravo AF: 0.209

Asia WGS AF: 0.114 AC: 399 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	9.5
DANN	Benign	0.80
PhyloP100		-0.027

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10980800;

hg19: chr9-113915905;