9-13683015-G-A

Position:

• chr9-13683015-G-A

Variant summary

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

The ENST00000664438.1(ENSG00000226197):​n.162+129691G>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 0.055 in 152,188 control chromosomes in the GnomAD database, including 466 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 0.055 (466 hom., cov: 32)
• Consequence: ENST00000664438.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

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 (AFR) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000664438.1	n.162+129691G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0548 AC: 8334 AN: 152070 Hom.: 459 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0265

Gnomad ASJ AF: 0.0309

Gnomad EAS AF: 0.0226

Gnomad SAS AF: 0.0951

Gnomad FIN AF: 0.0223

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0158

Gnomad OTH AF: 0.0483

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

GnomAD4 genome AF: 0.0550 AC: 8370 AN: 152188 Hom.: 466 Cov.: 32 AF XY: 0.0548 AC XY: 4078 AN XY: 74418

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.0265

Gnomad4 ASJ AF: 0.0309

Gnomad4 EAS AF: 0.0224

Gnomad4 SAS AF: 0.0949

Gnomad4 FIN AF: 0.0223

Gnomad4 NFE AF: 0.0158

Gnomad4 OTH AF: 0.0483

Alfa AF: 0.0411 Hom.: 38

Bravo AF: 0.0568

Asia WGS AF: 0.0650 AC: 226 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	2.9
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: rs10491761; hg19: chr9-13683014;