4-148943711-A-G

Variant names:

• chr4-148943711-A-G
• rs4835549
• ENST00000661928.1:n.347+76830A>G

Variant summary

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

The ENST00000661928.1(ENSG00000287292):​n.347+76830A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 152,062 control chromosomes in the GnomAD database, including 10,157 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 0.35 (10157 hom., cov: 32)
• Consequence: ENSG00000287292 ENST00000661928.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.420
• Publications: 3 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.516 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.347+76830A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52696 AN: 151944 Hom.: 10141 Cov.: 32

Gnomad AFR AF: 0.522

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.347 AC: 52764 AN: 152062 Hom.: 10157 Cov.: 32 AF XY: 0.343 AC XY: 25460 AN XY: 74330

African (AFR) AF: 0.522 AC: 21644 AN: 41456

American (AMR) AF: 0.367 AC: 5612 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1127 AN: 3464

East Asian (EAS) AF: 0.371 AC: 1921 AN: 5176

South Asian (SAS) AF: 0.259 AC: 1249 AN: 4816

European-Finnish (FIN) AF: 0.175 AC: 1857 AN: 10596

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18399 AN: 67972

Other (OTH) AF: 0.328 AC: 691 AN: 2108

Alfa AF: 0.321 Hom.: 1451

Bravo AF: 0.371

Asia WGS AF: 0.319 AC: 1106 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.8
DANN	Benign	0.72
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs4835549; hg19: chr4-149864863;