4-148943711-A-G

Position:

• chr4-148943711-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000287292 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986195	XR_001741441.2	n.3786+76830A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287292	ENST00000661928.1	n.347+76830A>G		intron_variant

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

Gnomad4 AFR AF: 0.522

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.328

Alfa AF: 0.315 Hom.: 1347

Bravo AF: 0.371

Asia WGS AF: 0.319 AC: 1106 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4835549; hg19: chr4-149864863;