9-73543838-A-T

Position:

• chr9-73543838-A-T

Variant summary

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

The ENST00000667966.1(ENSG00000286840):​n.269+4225T>A 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 0.845 in 152,078 control chromosomes in the GnomAD database, including 55,783 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 0.84 (55783 hom., cov: 33)
• Consequence: ENST00000667966.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.95 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+4225T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.845 AC: 128399 AN: 151960 Hom.: 55764 Cov.: 33

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.986

Gnomad AMR AF: 0.877

Gnomad ASJ AF: 0.909

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.921

Gnomad MID AF: 0.834

Gnomad NFE AF: 0.956

Gnomad OTH AF: 0.870

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

GnomAD4 genome AF: 0.845 AC: 128470 AN: 152078 Hom.: 55783 Cov.: 33 AF XY: 0.844 AC XY: 62751 AN XY: 74340

Gnomad4 AFR AF: 0.626

Gnomad4 AMR AF: 0.877

Gnomad4 ASJ AF: 0.909

Gnomad4 EAS AF: 0.778

Gnomad4 SAS AF: 0.872

Gnomad4 FIN AF: 0.921

Gnomad4 NFE AF: 0.956

Gnomad4 OTH AF: 0.872

Alfa AF: 0.896 Hom.: 3202

Bravo AF: 0.830

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.15
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs278714; hg19: chr9-76158754;