9-26281341-G-T

Variant names:

• chr9-26281341-G-T
• rs375658
• ENST00000844068.1:n.670-19973C>A

Variant summary

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

The ENST00000844068.1(ENSG00000309811):​n.670-19973C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 151,910 control chromosomes in the GnomAD database, including 26,455 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 0.58 (26455 hom., cov: 32)
• Consequence: ENSG00000309811 ENST00000844068.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.32
• Publications: 1 publications found

Genes affected

ENSG00000309811 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.09).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.833 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000844068.1. 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
	ENSG00000309811	ENST00000844068.1		n.670-19973C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.580 AC: 88060 AN: 151792 Hom.: 26415 Cov.: 32

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.855

Gnomad SAS AF: 0.739

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.580 AC: 88151 AN: 151910 Hom.: 26455 Cov.: 32 AF XY: 0.584 AC XY: 43317 AN XY: 74224

African (AFR) AF: 0.661 AC: 27386 AN: 41456

American (AMR) AF: 0.644 AC: 9822 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1454 AN: 3468

East Asian (EAS) AF: 0.854 AC: 4401 AN: 5152

South Asian (SAS) AF: 0.739 AC: 3563 AN: 4822

European-Finnish (FIN) AF: 0.485 AC: 5093 AN: 10498

Middle Eastern (MID) AF: 0.531 AC: 154 AN: 290

European-Non Finnish (NFE) AF: 0.512 AC: 34781 AN: 67950

Other (OTH) AF: 0.563 AC: 1187 AN: 2110

Alfa AF: 0.428 Hom.: 1220

Bravo AF: 0.592

Asia WGS AF: 0.796 AC: 2763 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.0070
DANN	Benign	0.18
PhyloP100		-5.3

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: rs375658;

hg19: chr9-26281339;

COSMIC: COSV60346643;