chr1-1161911-C-A

Position:

• chr1-1161911-C-A

Variant summary

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

The XR_007065351.1(LOC124903820):​n.1701C>A 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 0.234 in 152,200 control chromosomes in the GnomAD database, including 4,630 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 0.23 (4630 hom., cov: 35)
• Consequence: LOC124903820 XR_007065351.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.66

Genes affected

LOC124903820 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124903820	XR_007065351.1	n.1701C>A		non_coding_transcript_exon_variant	3/3
LOC124903820	XR_007065350.1	n.2419C>A		non_coding_transcript_exon_variant	2/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35602 AN: 152082 Hom.: 4629 Cov.: 35

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.0515

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.234 AC: 35619 AN: 152200 Hom.: 4630 Cov.: 35 AF XY: 0.233 AC XY: 17311 AN XY: 74430

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.0514

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.289

Gnomad4 OTH AF: 0.214

Alfa AF: 0.175 Hom.: 400

Bravo AF: 0.216

Asia WGS AF: 0.111 AC: 387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.0060
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs61768478; hg19: chr1-1097291;