2-153027501-A-C

Position:

• chr2-153027501-A-C

Variant summary

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

The XR_007087268.1(LOC105373691):​n.130-702A>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 0.341 in 151,824 control chromosomes in the GnomAD database, including 9,684 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 0.34 (9684 hom., cov: 31)
• Consequence: LOC105373691 XR_007087268.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.02

Genes affected

LOC105373691 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373691	XR_007087268.1	n.130-702A>C		intron_variant, non_coding_transcript_variant
LOC105373691	XR_007087267.1	n.194-702A>C		intron_variant, non_coding_transcript_variant
LOC105373691	XR_923481.1	n.310-702A>C		intron_variant, non_coding_transcript_variant
LOC105373691	XR_923482.2	n.246-702A>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51731 AN: 151706 Hom.: 9682 Cov.: 31

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.341 AC: 51750 AN: 151824 Hom.: 9684 Cov.: 31 AF XY: 0.335 AC XY: 24860 AN XY: 74210

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.340

Gnomad4 ASJ AF: 0.328

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.372

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.441

Gnomad4 OTH AF: 0.338

Alfa AF: 0.327 Hom.: 2425

Bravo AF: 0.330

Asia WGS AF: 0.262 AC: 910 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	8.5
DANN	Benign	0.95

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1435033; hg19: chr2-153884015;