4-148728881-G-A

Position:

• chr4-148728881-G-A

Variant summary

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

The ENST00000661928.1(ENSG00000287292):​n.223-137876G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 152,074 control chromosomes in the GnomAD database, including 5,721 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 (5721 hom., cov: 32)
• Consequence: ENST00000661928.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.181

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986195	XR_001741441.2	n.3662-137876G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000661928.1	n.223-137876G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37822 AN: 151956 Hom.: 5717 Cov.: 32

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.0626

Gnomad SAS AF: 0.152

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: 37854 AN: 152074 Hom.: 5721 Cov.: 32 AF XY: 0.241 AC XY: 17897 AN XY: 74348

Gnomad4 AFR AF: 0.427

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.0626

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.203

Gnomad4 OTH AF: 0.247

Alfa AF: 0.204 Hom.: 6991

Bravo AF: 0.263

Asia WGS AF: 0.115 AC: 402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	12
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17025017; hg19: chr4-149650033;