rs4675096

chr2-226804225-G-A

Variant summary

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

The ENST00000567305.1(ENSG00000261379):n.190G>A 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 0.209 in 152,088 control chromosomes in the GnomAD database, including 5,891 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 0.21 (5891 hom., cov: 32)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: ENST00000567305.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.255

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RHBDD1	XM_047445998.1	c.-3740G>A		5_prime_UTR_variant	1/8
RHBDD1	NM_001349069.2	c.-479-3261G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000567305.1	n.190G>A		non_coding_transcript_exon_variant	1/1
	ENST00000668519.1	n.78-3261G>A		intron_variant, non_coding_transcript_variant
	ENST00000607970.2	n.46+2870G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31646 AN: 151966 Hom.: 5864 Cov.: 32

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.0458

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.0840

Gnomad FIN AF: 0.0887

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0874

Gnomad OTH AF: 0.166

GnomAD4 exome AF: 0.250 AC: 1 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 NFE exome AF: 0.250

GnomAD4 genome AF: 0.209 AC: 31733 AN: 152084 Hom.: 5891 Cov.: 32 AF XY: 0.205 AC XY: 15260 AN XY: 74350

Gnomad4 AFR AF: 0.499

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.0458

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.0846

Gnomad4 FIN AF: 0.0887

Gnomad4 NFE AF: 0.0874

Gnomad4 OTH AF: 0.165

Alfa AF: 0.164 Hom.: 672

Bravo AF: 0.227

Asia WGS AF: 0.174 AC: 608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	7.6
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4675096; hg19: chr2-227668941;