rs2493864

Positions:

• chr1-178575868-C-A
• chr1-178575868-C-G
• chr1-178575868-C-T

Variant summary

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

The XR_922315.3(LOC105371632):​n.9993G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 152,164 control chromosomes in the GnomAD database, including 35,793 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 0.68 (35793 hom., cov: 34)
• Consequence: LOC105371632 XR_922315.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.605

Genes affected

LOC105371632 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105371632	XR_922315.3	n.9993G>T		non_coding_transcript_exon_variant	1/4
LOC105371632	XR_922313.3	n.9994G>T		non_coding_transcript_exon_variant	1/3
LOC105371632	XR_007066747.1	n.616-1887G>T		intron_variant, non_coding_transcript_variant
LOC105371632	XR_922314.3	n.616-2506G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.681 AC: 103481 AN: 152046 Hom.: 35729 Cov.: 34

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.703

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

GnomAD4 genome AF: 0.681 AC: 103608 AN: 152164 Hom.: 35793 Cov.: 34 AF XY: 0.683 AC XY: 50813 AN XY: 74396

Gnomad4 AFR AF: 0.804

Gnomad4 AMR AF: 0.712

Gnomad4 ASJ AF: 0.651

Gnomad4 EAS AF: 0.575

Gnomad4 SAS AF: 0.636

Gnomad4 FIN AF: 0.637

Gnomad4 NFE AF: 0.616

Gnomad4 OTH AF: 0.703

Alfa AF: 0.655 Hom.: 8367

Bravo AF: 0.696

Asia WGS AF: 0.639 AC: 2223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.6
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2493864; hg19: chr1-178545003;