9-16962021-G-C

Variant summary

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

The ENST00000649137.1(ENSG00000237153):n.412+3026G>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 0.86 in 152,154 control chromosomes in the GnomAD database, including 56,886 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 0.86 (56886 hom., cov: 32)
• Consequence: ENST00000649137.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.965 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000649137.1	n.412+3026G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.860 AC: 130804 AN: 152036 Hom.: 56860 Cov.: 32

Gnomad AFR AF: 0.719

Gnomad AMI AF: 0.930

Gnomad AMR AF: 0.932

Gnomad ASJ AF: 0.961

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.970

Gnomad FIN AF: 0.914

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.897

Gnomad OTH AF: 0.899

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

GnomAD4 genome AF: 0.860 AC: 130876 AN: 152154 Hom.: 56886 Cov.: 32 AF XY: 0.865 AC XY: 64380 AN XY: 74386

Gnomad4 AFR AF: 0.719

Gnomad4 AMR AF: 0.932

Gnomad4 ASJ AF: 0.961

Gnomad4 EAS AF: 0.988

Gnomad4 SAS AF: 0.970

Gnomad4 FIN AF: 0.914

Gnomad4 NFE AF: 0.897

Gnomad4 OTH AF: 0.901

Alfa AF: 0.872 Hom.: 6799

Bravo AF: 0.855

Asia WGS AF: 0.962 AC: 3347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.4
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: rs10511630; hg19: chr9-16962019;