chr1-1161911-C-A

Variant names:

• chr1-1161911-C-A
• rs61768478
• XR_007065350.1:n.2419C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007065350.1(LOC124903820):​n.2419C>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_007065350.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.66
• Publications: 3 publications found

Genes affected

LOC124903820 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.181 AC: 7514 AN: 41538

American (AMR) AF: 0.152 AC: 2319 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 704 AN: 3472

East Asian (EAS) AF: 0.0514 AC: 266 AN: 5176

South Asian (SAS) AF: 0.201 AC: 971 AN: 4824

European-Finnish (FIN) AF: 0.320 AC: 3392 AN: 10596

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.289 AC: 19677 AN: 67976

Other (OTH) AF: 0.214 AC: 452 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.0060
DANN	Benign	0.68
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs61768478; hg19: chr1-1097291;