rs10980800

chr9-111153625-T-C

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, non coding transcript 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: ENST00000426204.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270

Genes affected

(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/exons	MANE	UniProt
LOC105376219	XR_001746894.2	n.410-14006A>G		intron_variant, non_coding_transcript_variant
LOC105376219	XR_001746893.2	n.410-14006A>G		intron_variant, non_coding_transcript_variant
LOC105376219	XR_930247.3	n.410-14006A>G		intron_variant, non_coding_transcript_variant
LOC105376219	XR_930249.2	n.410-14006A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000426204.1	n.371-14006A>G		intron_variant, non_coding_transcript_variant		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;