rs360932

Positions:

• chr4-151987017-G-A

Variant summary

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

The ENST00000652265.1(ENSG00000286066):​n.1354+3555C>T 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 0.555 in 152,012 control chromosomes in the GnomAD database, including 24,436 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 0.55 (24436 hom., cov: 32)
• Consequence: ENST00000652265.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.576

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000652265.1	n.1354+3555C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84251 AN: 151894 Hom.: 24417 Cov.: 32

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.555 AC: 84305 AN: 152012 Hom.: 24436 Cov.: 32 AF XY: 0.541 AC XY: 40216 AN XY: 74294

Gnomad4 AFR AF: 0.461

Gnomad4 AMR AF: 0.545

Gnomad4 ASJ AF: 0.551

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.415

Gnomad4 FIN AF: 0.504

Gnomad4 NFE AF: 0.663

Gnomad4 OTH AF: 0.588

Alfa AF: 0.612 Hom.: 10318

Bravo AF: 0.556

Asia WGS AF: 0.335 AC: 1164 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.18
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs360932; hg19: chr4-152908169;