rs6725556

chr2-226802276-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+2054A>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 0.104 in 152,292 control chromosomes in the GnomAD database, including 1,163 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 0.10 (1163 hom., cov: 32)
• Consequence: ENST00000668519.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.791

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 (AFR) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RHBDD1	NM_001349069.2	c.-480+2054A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000668519.1	n.77+2054A>G		intron_variant, non_coding_transcript_variant
	ENST00000607970.2	n.46+921A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15800 AN: 152174 Hom.: 1160 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.0613

Gnomad ASJ AF: 0.0908

Gnomad EAS AF: 0.0135

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.0279

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0677

Gnomad OTH AF: 0.0910

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

GnomAD4 genome AF: 0.104 AC: 15825 AN: 152292 Hom.: 1163 Cov.: 32 AF XY: 0.102 AC XY: 7580 AN XY: 74478

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.0612

Gnomad4 ASJ AF: 0.0908

Gnomad4 EAS AF: 0.0135

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.0279

Gnomad4 NFE AF: 0.0678

Gnomad4 OTH AF: 0.0934

Alfa AF: 0.0748 Hom.: 726

Bravo AF: 0.108

Asia WGS AF: 0.0760 AC: 266 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	8.8
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6725556; hg19: chr2-227666992;