rs6725330

Positions:

• chr2-226802141-A-G

Variant summary

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

The ENST00000668519.1(ENSG00000272622):​n.77+1919A>G 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 0.14 in 152,116 control chromosomes in the GnomAD database, including 1,664 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 0.14 (1664 hom., cov: 32)
• Consequence: ENST00000668519.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.277

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RHBDD1	NM_001349069.2	c.-480+1919A>G		intron_variant			NP_001335998.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000668519.1	n.77+1919A>G		intron_variant, non_coding_transcript_variant
	ENST00000607970.2	n.46+786A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21293 AN: 151998 Hom.: 1659 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.0907

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.0720

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.140 AC: 21324 AN: 152116 Hom.: 1664 Cov.: 32 AF XY: 0.140 AC XY: 10408 AN XY: 74360

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.0911

Gnomad4 SAS AF: 0.245

Gnomad4 FIN AF: 0.0720

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.141

Alfa AF: 0.127 Hom.: 1859

Bravo AF: 0.144

Asia WGS AF: 0.166 AC: 578 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.9
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6725330; hg19: chr2-227666857;