rs2605393

Positions:

• chr3-36368109-T-G

Variant summary

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

The XR_007095868.1(LOC124906227):​n.148-32404A>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 0.386 in 151,962 control chromosomes in the GnomAD database, including 12,883 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 0.39 (12883 hom., cov: 32)
• Consequence: LOC124906227 XR_007095868.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.506

Genes affected

LOC124906227 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124906227	XR_007095868.1	n.148-32404A>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58635 AN: 151844 Hom.: 12849 Cov.: 32

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.386 AC: 58716 AN: 151962 Hom.: 12883 Cov.: 32 AF XY: 0.382 AC XY: 28364 AN XY: 74286

Gnomad4 AFR AF: 0.619

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.289

Gnomad4 EAS AF: 0.303

Gnomad4 SAS AF: 0.343

Gnomad4 FIN AF: 0.258

Gnomad4 NFE AF: 0.290

Gnomad4 OTH AF: 0.376

Alfa AF: 0.311 Hom.: 8764

Bravo AF: 0.403

Asia WGS AF: 0.329 AC: 1145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.7
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2605393; hg19: chr3-36409601;