rs1876054

Positions:

• chr4-132117054-A-G
• chr4-132117054-A-T

Variant summary

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

The ENST00000652009.1(ENSG00000251598):​n.178-88573T>C 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 0.515 in 151,662 control chromosomes in the GnomAD database, including 20,123 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 0.52 (20123 hom., cov: 31)
• Consequence: ENST00000652009.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000652009.1	n.178-88573T>C		intron_variant, non_coding_transcript_variant
	ENST00000420721.2	n.181+6797T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.515 AC: 78068 AN: 151544 Hom.: 20094 Cov.: 31

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.515 AC: 78154 AN: 151662 Hom.: 20123 Cov.: 31 AF XY: 0.514 AC XY: 38105 AN XY: 74086

Gnomad4 AFR AF: 0.545

Gnomad4 AMR AF: 0.483

Gnomad4 ASJ AF: 0.604

Gnomad4 EAS AF: 0.519

Gnomad4 SAS AF: 0.501

Gnomad4 FIN AF: 0.490

Gnomad4 NFE AF: 0.504

Gnomad4 OTH AF: 0.511

Alfa AF: 0.509 Hom.: 3320

Bravo AF: 0.517

Asia WGS AF: 0.478 AC: 1658 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.37
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1876054; hg19: chr4-133038209;