chr4-148731947-C-A

Variant names:

• chr4-148731947-C-A
• rs10030849
• ENST00000661928.1:n.223-134810C>A

Variant summary

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

The ENST00000661928.1(ENSG00000287292):​n.223-134810C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 152,062 control chromosomes in the GnomAD database, including 5,715 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 0.25 (5715 hom., cov: 31)
• Consequence: ENSG00000287292 ENST00000661928.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.999
• Publications: 4 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.422 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287292	ENST00000661928.1		n.223-134810C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37812 AN: 151944 Hom.: 5711 Cov.: 31

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.0634

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.249 AC: 37845 AN: 152062 Hom.: 5715 Cov.: 31 AF XY: 0.241 AC XY: 17894 AN XY: 74344

African (AFR) AF: 0.427 AC: 17703 AN: 41460

American (AMR) AF: 0.173 AC: 2647 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 654 AN: 3468

East Asian (EAS) AF: 0.0633 AC: 327 AN: 5164

South Asian (SAS) AF: 0.150 AC: 723 AN: 4814

European-Finnish (FIN) AF: 0.116 AC: 1232 AN: 10580

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

European-Non Finnish (NFE) AF: 0.203 AC: 13820 AN: 67984

Other (OTH) AF: 0.246 AC: 520 AN: 2112

Alfa AF: 0.229 Hom.: 584

Bravo AF: 0.263

Asia WGS AF: 0.115 AC: 402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.92
DANN	Benign	0.28
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs10030849; hg19: chr4-149653099;