chr1-1159358-A-G

Position:

• chr1-1159358-A-G

Variant summary

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

The XR_007065351.1(LOC124903820):​n.278+674A>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 0.61 in 152,008 control chromosomes in the GnomAD database, including 28,796 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 0.61 (28796 hom., cov: 33)
• Consequence: LOC124903820 XR_007065351.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.960

Genes affected

LOC124903820 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124903820	XR_007065351.1	n.278+674A>G		intron_variant, non_coding_transcript_variant
LOC124903820	XR_007065350.1	n.996+674A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92583 AN: 151890 Hom.: 28762 Cov.: 33

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.724

Gnomad AMR AF: 0.731

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.635

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

GnomAD4 genome AF: 0.610 AC: 92662 AN: 152008 Hom.: 28796 Cov.: 33 AF XY: 0.610 AC XY: 45319 AN XY: 74280

Gnomad4 AFR AF: 0.517

Gnomad4 AMR AF: 0.731

Gnomad4 ASJ AF: 0.698

Gnomad4 EAS AF: 0.537

Gnomad4 SAS AF: 0.672

Gnomad4 FIN AF: 0.576

Gnomad4 NFE AF: 0.638

Gnomad4 OTH AF: 0.639

Alfa AF: 0.630 Hom.: 17902

Bravo AF: 0.616

Asia WGS AF: 0.625 AC: 2175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4970362; hg19: chr1-1094738; COSMIC: COSV52468699;