rs6733000

Positions:

• chr2-21729332-C-T

Variant summary

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

The ENST00000435237.1(ENSG00000233005):​n.194-70025C>T 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 0.102 in 152,026 control chromosomes in the GnomAD database, including 937 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 (937 hom., cov: 32)
• Consequence: ENST00000435237.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000435237.1	n.194-70025C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15485 AN: 151908 Hom.: 928 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0964

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.0343

Gnomad SAS AF: 0.0559

Gnomad FIN AF: 0.0567

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0819

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.102 AC: 15518 AN: 152026 Hom.: 937 Cov.: 32 AF XY: 0.0999 AC XY: 7426 AN XY: 74310

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.0961

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.0344

Gnomad4 SAS AF: 0.0557

Gnomad4 FIN AF: 0.0567

Gnomad4 NFE AF: 0.0819

Gnomad4 OTH AF: 0.110

Alfa AF: 0.0857 Hom.: 295

Bravo AF: 0.109

Asia WGS AF: 0.0690 AC: 241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6733000; hg19: chr2-21952204;