9-79167270-A-G

Position:

• chr9-79167270-A-G

Variant summary

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

The ENST00000650036.1(ENSG00000260995):​n.403+15916T>C 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 0.678 in 151,966 control chromosomes in the GnomAD database, including 35,374 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 0.68 (35374 hom., cov: 31)
• Consequence: ENST00000650036.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.121

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.743 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
	ENST00000650036.1	n.403+15916T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.678 AC: 103022 AN: 151848 Hom.: 35360 Cov.: 31

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.746

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.762

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.714

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

GnomAD4 genome AF: 0.678 AC: 103075 AN: 151966 Hom.: 35374 Cov.: 31 AF XY: 0.677 AC XY: 50313 AN XY: 74268

Gnomad4 AFR AF: 0.750

Gnomad4 AMR AF: 0.746

Gnomad4 ASJ AF: 0.733

Gnomad4 EAS AF: 0.763

Gnomad4 SAS AF: 0.565

Gnomad4 FIN AF: 0.617

Gnomad4 NFE AF: 0.626

Gnomad4 OTH AF: 0.712

Alfa AF: 0.643 Hom.: 57940

Bravo AF: 0.694

Asia WGS AF: 0.639 AC: 2222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1361536; hg19: chr9-81782185;