1-1163334-C-G

Position:

• chr1-1163334-C-G

Variant summary

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

The XR_007065348.1(LOC124903818):​n.382+76C>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 0.495 in 152,092 control chromosomes in the GnomAD database, including 20,011 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 0.50 (20011 hom., cov: 34)
• Consequence: LOC124903818 XR_007065348.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300

Genes affected

LOC124903818 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124903818	XR_007065348.1	n.382+76C>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.495 AC: 75266 AN: 151974 Hom.: 20001 Cov.: 34

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.660

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.495 AC: 75304 AN: 152092 Hom.: 20011 Cov.: 34 AF XY: 0.489 AC XY: 36392 AN XY: 74350

Gnomad4 AFR AF: 0.323

Gnomad4 AMR AF: 0.639

Gnomad4 ASJ AF: 0.601

Gnomad4 EAS AF: 0.288

Gnomad4 SAS AF: 0.450

Gnomad4 FIN AF: 0.473

Gnomad4 NFE AF: 0.581

Gnomad4 OTH AF: 0.526

Alfa AF: 0.372 Hom.: 993

Bravo AF: 0.500

Asia WGS AF: 0.367 AC: 1281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4379629; hg19: chr1-1098714;