rs10992471

Variant names:

• chr9-92797223-G-A
• rs10992471
• ENST00000738777.1:n.354G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000738777.1(ENSG00000296403):​n.354G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 151,988 control chromosomes in the GnomAD database, including 16,694 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 0.45 (16694 hom., cov: 31)
• Consequence: ENSG00000296403 ENST00000738777.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110
• Publications: 13 publications found

Genes affected

ENSG00000296403 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000738777.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296403	ENST00000738777.1		n.354G>A		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000296403	ENST00000738778.1		n.350G>A		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67952 AN: 151870 Hom.: 16666 Cov.: 31

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.0988

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.448 AC: 68016 AN: 151988 Hom.: 16694 Cov.: 31 AF XY: 0.440 AC XY: 32661 AN XY: 74270

African (AFR) AF: 0.641 AC: 26556 AN: 41450

American (AMR) AF: 0.330 AC: 5032 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1518 AN: 3470

East Asian (EAS) AF: 0.0993 AC: 514 AN: 5178

South Asian (SAS) AF: 0.276 AC: 1328 AN: 4820

European-Finnish (FIN) AF: 0.375 AC: 3956 AN: 10558

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.405 AC: 27546 AN: 67938

Other (OTH) AF: 0.434 AC: 914 AN: 2108

Alfa AF: 0.421 Hom.: 43710

Bravo AF: 0.455

Asia WGS AF: 0.206 AC: 717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.88
DANN	Benign	0.31
PhyloP100		-0.011

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10992471;

hg19: chr9-95559505;