rs6532183

Positions:

• chr4-89684903-A-G

Variant summary

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

The ENST00000612706.1(ENSG00000251095):​n.621A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 152,188 control chromosomes in the GnomAD database, including 3,038 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 0.15 (3038 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000251095 ENST00000612706.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145

Genes affected

ENSG00000251095 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124900602	XR_001741764.2	n.3399A>G		non_coding_transcript_exon_variant	1/3
LOC124900602	XR_007058465.1	n.3399A>G		non_coding_transcript_exon_variant	1/2
LOC124900602	XR_007058466.1	n.3399A>G		non_coding_transcript_exon_variant	1/3
LOC124900602	XR_938983.2	n.3399A>G		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000251095	ENST00000612706.1	n.621A>G		non_coding_transcript_exon_variant	2/2	5
ENSG00000251095	ENST00000506864.5	n.472-6382A>G		intron_variant		4
ENSG00000251095	ENST00000507916.6	n.135-6382A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23522 AN: 152070 Hom.: 3024 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.0776

Gnomad ASJ AF: 0.0646

Gnomad EAS AF: 0.0520

Gnomad SAS AF: 0.0879

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.0782

Gnomad OTH AF: 0.127

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.155 AC: 23559 AN: 152188 Hom.: 3038 Cov.: 32 AF XY: 0.153 AC XY: 11358 AN XY: 74430

Gnomad4 AFR AF: 0.352

Gnomad4 AMR AF: 0.0774

Gnomad4 ASJ AF: 0.0646

Gnomad4 EAS AF: 0.0523

Gnomad4 SAS AF: 0.0874

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.0782

Gnomad4 OTH AF: 0.131

Alfa AF: 0.0903 Hom.: 653

Bravo AF: 0.161

Asia WGS AF: 0.101 AC: 352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.7
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6532183; hg19: chr4-90606054;