9-84494571-A-C

Position:

• chr9-84494571-A-C

Variant summary

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

The ENST00000650453.1(ENSG00000285987):​n.537-2898A>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 0.0433 in 152,264 control chromosomes in the GnomAD database, including 248 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 0.043 (248 hom., cov: 33)
• Consequence: ENST00000650453.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.487

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0934 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102724036	XR_007061623.1	n.158-2898A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000650453.1	n.537-2898A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0433 AC: 6590 AN: 152146 Hom.: 246 Cov.: 33

Gnomad AFR AF: 0.00982

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.0906

Gnomad ASJ AF: 0.0147

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.0306

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0392

Gnomad OTH AF: 0.0411

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

GnomAD4 genome AF: 0.0433 AC: 6596 AN: 152264 Hom.: 248 Cov.: 33 AF XY: 0.0471 AC XY: 3505 AN XY: 74446

Gnomad4 AFR AF: 0.00979

Gnomad4 AMR AF: 0.0910

Gnomad4 ASJ AF: 0.0147

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.0304

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.0392

Gnomad4 OTH AF: 0.0406

Alfa AF: 0.0235 Hom.: 19

Bravo AF: 0.0427

Asia WGS AF: 0.0670 AC: 230 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.5
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10512148; hg19: chr9-87109486;