rs1510107

Positions:

• chr2-52932999-C-G

Variant summary

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

The ENST00000421575.6(ENSG00000228033):​n.85-22975G>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 0.714 in 151,758 control chromosomes in the GnomAD database, including 40,158 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 0.71 (40158 hom., cov: 30)
• Consequence: ENST00000421575.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.10

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.912 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105369165	XR_002959384.2	n.49-22975G>C		intron_variant, non_coding_transcript_variant
LOC105369165	XR_001739464.3	n.205+1406G>C		intron_variant, non_coding_transcript_variant
LOC105369165	XR_002959385.2	n.205+1406G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000421575.6	n.85-22975G>C		intron_variant, non_coding_transcript_variant		5
	ENST00000668945.1	n.96+1406G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.714 AC: 108230 AN: 151640 Hom.: 40093 Cov.: 30

Gnomad AFR AF: 0.920

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.714 AC: 108361 AN: 151758 Hom.: 40158 Cov.: 30 AF XY: 0.712 AC XY: 52784 AN XY: 74100

Gnomad4 AFR AF: 0.920

Gnomad4 AMR AF: 0.648

Gnomad4 ASJ AF: 0.606

Gnomad4 EAS AF: 0.432

Gnomad4 SAS AF: 0.804

Gnomad4 FIN AF: 0.680

Gnomad4 NFE AF: 0.634

Gnomad4 OTH AF: 0.670

Alfa AF: 0.704 Hom.: 4766

Bravo AF: 0.713

Asia WGS AF: 0.685 AC: 2379 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.041
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1510107; hg19: chr2-53160137;