9-21771242-T-C

Variant names:

• chr9-21771242-T-C
• rs1341866
• ENST00000765951.1:n.155-19602T>C

Variant summary

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

The ENST00000765951.1(ENSG00000299739):​n.155-19602T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 152,026 control chromosomes in the GnomAD database, including 10,006 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 0.35 (10006 hom., cov: 32)
• Consequence: ENSG00000299739 ENST00000765951.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31
• Publications: 9 publications found

Genes affected

ENSG00000299739 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000765951.1. 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
	ENSG00000299739	ENST00000765951.1		n.155-19602T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52569 AN: 151906 Hom.: 9999 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.346 AC: 52609 AN: 152026 Hom.: 10006 Cov.: 32 AF XY: 0.346 AC XY: 25685 AN XY: 74298

African (AFR) AF: 0.184 AC: 7632 AN: 41484

American (AMR) AF: 0.393 AC: 5997 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1333 AN: 3468

East Asian (EAS) AF: 0.434 AC: 2236 AN: 5154

South Asian (SAS) AF: 0.270 AC: 1303 AN: 4822

European-Finnish (FIN) AF: 0.418 AC: 4415 AN: 10564

Middle Eastern (MID) AF: 0.291 AC: 85 AN: 292

European-Non Finnish (NFE) AF: 0.422 AC: 28697 AN: 67950

Other (OTH) AF: 0.344 AC: 726 AN: 2110

Alfa AF: 0.394 Hom.: 7469

Bravo AF: 0.340

Asia WGS AF: 0.323 AC: 1123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.23
DANN	Benign	0.45
PhyloP100		-1.3

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: rs1341866;

hg19: chr9-21771241;