rs9643449

Variant names:

• chr8-82758572-A-G
• rs9643449
• ENST00000658531.1:n.254-145083A>G

Your query was ambiguous. Multiple possible variants found:

• chr8-82758572-A-G
• chr8-82758572-A-T

Variant summary

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

The ENST00000658531.1(ENSG00000254394):​n.254-145083A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.654 in 152,002 control chromosomes in the GnomAD database, including 32,684 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 0.65 (32684 hom., cov: 32)
• Consequence: ENSG00000254394 ENST00000658531.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792
• Publications: 6 publications found

Genes affected

ENSG00000254394 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.668 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000658531.1. 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
	ENSG00000254394	ENST00000658531.1		n.254-145083A>G		intron	N/A
	ENSG00000254394	ENST00000663058.1		n.944-154367A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.653 AC: 99231 AN: 151882 Hom.: 32634 Cov.: 32

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.654 AC: 99339 AN: 152002 Hom.: 32684 Cov.: 32 AF XY: 0.652 AC XY: 48462 AN XY: 74296

African (AFR) AF: 0.675 AC: 27968 AN: 41454

American (AMR) AF: 0.599 AC: 9142 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1791 AN: 3472

East Asian (EAS) AF: 0.457 AC: 2345 AN: 5128

South Asian (SAS) AF: 0.672 AC: 3233 AN: 4814

European-Finnish (FIN) AF: 0.688 AC: 7278 AN: 10574

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.670 AC: 45517 AN: 67972

Other (OTH) AF: 0.651 AC: 1374 AN: 2112

Alfa AF: 0.657 Hom.: 95489

Bravo AF: 0.645

Asia WGS AF: 0.589 AC: 2055 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	2.1
DANN	Benign	0.38
PhyloP100		-0.79

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: rs9643449;

hg19: chr8-83670807;