rs6436635

Positions:

• chr2-226800962-G-A
• chr2-226800962-G-C

Variant summary

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

The ENST00000668519.1(ENSG00000272622):​n.77+740G>A 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 0.0662 in 152,226 control chromosomes in the GnomAD database, including 639 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 0.066 (639 hom., cov: 32)
• Consequence: ENST00000668519.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.321

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RHBDD1	NM_001349069.2	c.-480+740G>A		intron_variant			NP_001335998.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000668519.1	n.77+740G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0662 AC: 10066 AN: 152108 Hom.: 634 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0639

Gnomad ASJ AF: 0.0432

Gnomad EAS AF: 0.0300

Gnomad SAS AF: 0.0230

Gnomad FIN AF: 0.0275

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0194

Gnomad OTH AF: 0.0603

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

GnomAD4 genome AF: 0.0662 AC: 10080 AN: 152226 Hom.: 639 Cov.: 32 AF XY: 0.0650 AC XY: 4839 AN XY: 74448

Gnomad4 AFR AF: 0.167

Gnomad4 AMR AF: 0.0642

Gnomad4 ASJ AF: 0.0432

Gnomad4 EAS AF: 0.0305

Gnomad4 SAS AF: 0.0228

Gnomad4 FIN AF: 0.0275

Gnomad4 NFE AF: 0.0194

Gnomad4 OTH AF: 0.0606

Alfa AF: 0.0291 Hom.: 42

Bravo AF: 0.0750

Asia WGS AF: 0.0340 AC: 119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	11
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6436635; hg19: chr2-227665678;