4-148634967-C-G

Variant names:

• chr4-148634967-C-G
• rs6845733
• ENST00000661928.1:n.222+90383C>G

Variant summary

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

The ENST00000661928.1(ENSG00000287292):​n.222+90383C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 151,846 control chromosomes in the GnomAD database, including 17,523 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 0.47 (17523 hom., cov: 32)
• Consequence: ENSG00000287292 ENST00000661928.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.534
• Publications: 1 publications found

Genes affected

ENSG00000287292 (HGNC:58892):

LOC107986195 (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 (EAS) allele frequency at 95% confidence interval = 0.886 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000661928.1. 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
	ENSG00000287292	ENST00000661928.1		n.222+90383C>G		intron	N/A
	ENSG00000287292	ENST00000817567.1		n.371-6624C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70924 AN: 151728 Hom.: 17494 Cov.: 32

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.907

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.468 AC: 71011 AN: 151846 Hom.: 17523 Cov.: 32 AF XY: 0.480 AC XY: 35624 AN XY: 74200

African (AFR) AF: 0.409 AC: 16912 AN: 41372

American (AMR) AF: 0.576 AC: 8781 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1246 AN: 3468

East Asian (EAS) AF: 0.907 AC: 4682 AN: 5160

South Asian (SAS) AF: 0.630 AC: 3026 AN: 4806

European-Finnish (FIN) AF: 0.539 AC: 5675 AN: 10528

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.431 AC: 29298 AN: 67944

Other (OTH) AF: 0.437 AC: 922 AN: 2112

Alfa AF: 0.283 Hom.: 662

Bravo AF: 0.468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.60
DANN	Benign	0.35
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs6845733; hg19: chr4-149556119;