rs914051

Positions:

• chr9-17062836-G-A
• chr9-17062836-G-C

Variant summary

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

The ENST00000430545.4(ENSG00000237153):​n.393+13795G>A 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 0.432 in 151,968 control chromosomes in the GnomAD database, including 14,593 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 0.43 (14593 hom., cov: 32)
• Consequence: ENST00000430545.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000430545.4	n.393+13795G>A		intron_variant, non_coding_transcript_variant		5
	ENST00000649821.1	n.179+9836G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65616 AN: 151850 Hom.: 14566 Cov.: 32

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.432 AC: 65689 AN: 151968 Hom.: 14593 Cov.: 32 AF XY: 0.418 AC XY: 31016 AN XY: 74262

Gnomad4 AFR AF: 0.490

Gnomad4 AMR AF: 0.361

Gnomad4 ASJ AF: 0.553

Gnomad4 EAS AF: 0.307

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.311

Gnomad4 NFE AF: 0.449

Gnomad4 OTH AF: 0.441

Alfa AF: 0.436 Hom.: 1798

Bravo AF: 0.444

Asia WGS AF: 0.291 AC: 1011 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	5.9
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs914051; hg19: chr9-17062834;