8-9956901-A-G

Variant names:

• chr8-9956901-A-G
• rs656319
• ENST00000843628.1:n.219-7985A>G

Variant summary

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

The ENST00000843628.1(ENSG00000309740):​n.219-7985A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 152,004 control chromosomes in the GnomAD database, including 18,963 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 0.49 (18963 hom., cov: 32)
• Consequence: ENSG00000309740 ENST00000843628.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.518
• Publications: 15 publications found

Genes affected

ENSG00000309740 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000843628.1. 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
	ENSG00000309740	ENST00000843628.1		n.219-7985A>G		intron	N/A
	ENSG00000309740	ENST00000843629.1		n.296-7985A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74254 AN: 151886 Hom.: 18954 Cov.: 32

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.0530

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.489 AC: 74299 AN: 152004 Hom.: 18963 Cov.: 32 AF XY: 0.478 AC XY: 35542 AN XY: 74318

African (AFR) AF: 0.453 AC: 18767 AN: 41410

American (AMR) AF: 0.472 AC: 7213 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.599 AC: 2081 AN: 3472

East Asian (EAS) AF: 0.0533 AC: 276 AN: 5178

South Asian (SAS) AF: 0.376 AC: 1807 AN: 4812

European-Finnish (FIN) AF: 0.427 AC: 4517 AN: 10572

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.559 AC: 37987 AN: 67950

Other (OTH) AF: 0.523 AC: 1104 AN: 2112

Alfa AF: 0.530 Hom.: 46390

Bravo AF: 0.486

Asia WGS AF: 0.253 AC: 882 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.4
DANN	Benign	0.49
PhyloP100		0.52

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: rs656319;

hg19: chr8-9814411;