chr9-111214463-T-C

Position:

• chr9-111214463-T-C

Variant summary

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

The ENST00000426204.1(ENSG00000227531):​n.370+58350A>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 0.214 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: ENST00000426204.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105376219	XR_001746894.2	n.409+58350A>G		intron_variant, non_coding_transcript_variant
LOC105376219	XR_001746893.2	n.409+58350A>G		intron_variant, non_coding_transcript_variant
LOC105376219	XR_930247.3	n.409+58350A>G		intron_variant, non_coding_transcript_variant
LOC105376219	XR_930249.2	n.409+58350A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000426204.1	n.370+58350A>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.0985

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.243

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.278

Gnomad4 OTH AF: 0.232

Alfa AF: 0.260 Hom.: 8856

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs700131; hg19: chr9-113976743;