rs9957673

Variant names:

• chr18-59899156-C-T
• rs9957673
• ENST00000848866.1:n.218+860G>A

Variant summary

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

The ENST00000848866.1(ENSG00000310295):​n.218+860G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,124 control chromosomes in the GnomAD database, including 4,527 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 0.22 (4527 hom., cov: 32)
• Consequence: ENSG00000310295 ENST00000848866.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.681
• Publications: 8 publications found

Genes affected

ENSG00000310295 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000848866.1. 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
	ENSG00000310295	ENST00000848866.1		n.218+860G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33298 AN: 152006 Hom.: 4513 Cov.: 32

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.0627

Gnomad SAS AF: 0.0819

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.219 AC: 33346 AN: 152124 Hom.: 4527 Cov.: 32 AF XY: 0.218 AC XY: 16201 AN XY: 74382

African (AFR) AF: 0.374 AC: 15512 AN: 41472

American (AMR) AF: 0.124 AC: 1903 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 420 AN: 3472

East Asian (EAS) AF: 0.0626 AC: 325 AN: 5190

South Asian (SAS) AF: 0.0815 AC: 394 AN: 4832

European-Finnish (FIN) AF: 0.260 AC: 2755 AN: 10576

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11527 AN: 67974

Other (OTH) AF: 0.186 AC: 392 AN: 2106

Alfa AF: 0.179 Hom.: 7180

Bravo AF: 0.217

Asia WGS AF: 0.0940 AC: 327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.67
DANN	Benign	0.75
PhyloP100		-0.68

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: rs9957673;

hg19: chr18-57566388;