rs1356702

Positions:

• chr2-221640484-A-G
• chr2-221640484-A-T

Variant summary

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

The ENST00000658881.1(ENSG00000234446):​n.115-1124A>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 0.219 in 152,100 control chromosomes in the GnomAD database, including 3,843 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 0.22 (3843 hom., cov: 32)
• Consequence: ENST00000658881.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330

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 (EAS) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105373899	XR_923942.1	n.70-1124A>G		intron_variant, non_coding_transcript_variant
LOC105373899	XR_001739234.1	n.107-1124A>G		intron_variant, non_coding_transcript_variant
LOC105373899	XR_001739235.1	n.70-1124A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000658881.1	n.115-1124A>G		intron_variant, non_coding_transcript_variant
	ENST00000453706.2	n.56-1124A>G		intron_variant, non_coding_transcript_variant		5
	ENST00000664786.1	n.61-1124A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33333 AN: 151982 Hom.: 3833 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.219 AC: 33385 AN: 152100 Hom.: 3843 Cov.: 32 AF XY: 0.224 AC XY: 16657 AN XY: 74370

Gnomad4 AFR AF: 0.246

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.368

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.211

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.248

Alfa AF: 0.205 Hom.: 391

Bravo AF: 0.223

Asia WGS AF: 0.296 AC: 1026 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1356702; hg19: chr2-222505204;