rs350729

chr2-52756635-T-G

Variant summary

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

The ENST00000421575.6(ENSG00000228033):n.208-23858A>C 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 0.654 in 151,998 control chromosomes in the GnomAD database, including 32,803 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 0.65 (32803 hom., cov: 32)
• Consequence: ENST00000421575.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.280

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369165	XR_002959384.2	n.172-29817A>C		intron_variant, non_coding_transcript_variant
LOC105369165	XR_001739464.3	n.329-23858A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000421575.6	n.208-23858A>C		intron_variant, non_coding_transcript_variant		5
	ENST00000443237.1	n.120-29817A>C		intron_variant, non_coding_transcript_variant		3
	ENST00000668945.1	n.220-29817A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99347 AN: 151880 Hom.: 32792 Cov.: 32

Gnomad AFR AF: 0.651

Gnomad AMI AF: 0.917

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.654 AC: 99397 AN: 151998 Hom.: 32803 Cov.: 32 AF XY: 0.650 AC XY: 48275 AN XY: 74256

Gnomad4 AFR AF: 0.650

Gnomad4 AMR AF: 0.619

Gnomad4 ASJ AF: 0.691

Gnomad4 EAS AF: 0.465

Gnomad4 SAS AF: 0.585

Gnomad4 FIN AF: 0.653

Gnomad4 NFE AF: 0.677

Gnomad4 OTH AF: 0.686

Alfa AF: 0.638 Hom.: 4907

Bravo AF: 0.651

Asia WGS AF: 0.548 AC: 1911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	2.9
Dann	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs350729; hg19: chr2-52983773;