rs1160297

Positions:

• chr2-53010182-G-C
• chr2-53010182-G-T

Variant summary

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

The XR_002959384.2(LOC105369165):​n.49-100158C>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 0.69 in 151,974 control chromosomes in the GnomAD database, including 37,125 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 0.69 (37125 hom., cov: 32)
• Consequence: LOC105369165 XR_002959384.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.421

Genes affected

LOC105369165 (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 = 0.853 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369165	XR_002959384.2	n.49-100158C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.689 AC: 104674 AN: 151856 Hom.: 37071 Cov.: 32

Gnomad AFR AF: 0.861

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.644

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

GnomAD4 genome AF: 0.690 AC: 104791 AN: 151974 Hom.: 37125 Cov.: 32 AF XY: 0.689 AC XY: 51165 AN XY: 74264

Gnomad4 AFR AF: 0.861

Gnomad4 AMR AF: 0.634

Gnomad4 ASJ AF: 0.578

Gnomad4 EAS AF: 0.510

Gnomad4 SAS AF: 0.790

Gnomad4 FIN AF: 0.668

Gnomad4 NFE AF: 0.618

Gnomad4 OTH AF: 0.648

Alfa AF: 0.623 Hom.: 16569

Bravo AF: 0.687

Asia WGS AF: 0.697 AC: 2423 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	2.7
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1160297; hg19: chr2-53237320;