chr4-148713799-A-G

Position:

• chr4-148713799-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000661928.1(ENSG00000287292):​n.223-152958A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 151,912 control chromosomes in the GnomAD database, including 26,081 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 0.56 (26081 hom., cov: 31)
• Consequence: ENSG00000287292 ENST00000661928.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.496

Genes affected

ENSG00000287292 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986195	XR_001741441.2	n.3662-152958A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287292	ENST00000661928.1	n.223-152958A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.561 AC: 85185 AN: 151798 Hom.: 26050 Cov.: 31

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.561 AC: 85259 AN: 151912 Hom.: 26081 Cov.: 31 AF XY: 0.552 AC XY: 40999 AN XY: 74218

Gnomad4 AFR AF: 0.795

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.615

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.338

Gnomad4 FIN AF: 0.494

Gnomad4 NFE AF: 0.511

Gnomad4 OTH AF: 0.583

Alfa AF: 0.536 Hom.: 2706

Bravo AF: 0.566

Asia WGS AF: 0.267 AC: 930 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.82
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10519979; hg19: chr4-149634951;