rs228173

Positions:

• chr1-143405602-T-C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The XR_001738207.2(LOC107985200):​n.257+14471A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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 0.11 (2 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: LOC107985200 XR_001738207.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98

Genes affected

LOC107985200 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985200	XR_001738207.2	n.257+14471A>G		intron_variant, non_coding_transcript_variant
LOC107985200	XR_001738208.2	n.287-3822A>G		intron_variant, non_coding_transcript_variant
LOC107985200	XR_007066535.1	n.259-11916A>G		intron_variant, non_coding_transcript_variant
LOC107985200	XR_007066536.1	n.263+14471A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.00 AC: 655 AN: 6080 Hom.: 2 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.0455

Gnomad AMR AF: 0.0783

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.0425

Gnomad SAS AF: 0.0863

Gnomad FIN AF: 0.00658

Gnomad MID AF: 0.0588

Gnomad NFE AF: 0.0690

Gnomad OTH AF: 0.152

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.108 AC: 659 AN: 6080 Hom.: 2 Cov.: 0 AF XY: 0.100 AC XY: 278 AN XY: 2772

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.0761

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.0427

Gnomad4 SAS AF: 0.0833

Gnomad4 FIN AF: 0.00658

Gnomad4 NFE AF: 0.0683

Gnomad4 OTH AF: 0.141

Alfa AF: 0.254 Hom.: 90

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	6.4

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs228173; hg19: chr1-148947423;