chr9-73543766-G-A

Position:

• chr9-73543766-G-A

Variant summary

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

The ENST00000667966.1(ENSG00000286840):​n.269+4297C>T 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 0.124 in 152,028 control chromosomes in the GnomAD database, including 1,482 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 0.12 (1482 hom., cov: 33)
• Consequence: ENST00000667966.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.154

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.168 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
	ENST00000667966.1	n.269+4297C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18906 AN: 151910 Hom.: 1477 Cov.: 33

Gnomad AFR AF: 0.0311

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.0975

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.124 AC: 18916 AN: 152028 Hom.: 1482 Cov.: 33 AF XY: 0.125 AC XY: 9296 AN XY: 74302

Gnomad4 AFR AF: 0.0310

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.0970

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.157

Alfa AF: 0.157 Hom.: 2194

Bravo AF: 0.118

Asia WGS AF: 0.104 AC: 358 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.9
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11143609; hg19: chr9-76158682;