chr1-1161907-T-C

Variant names:

• chr1-1161907-T-C
• rs9442384
• XR_007065350.1:n.2415T>C

Variant summary

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

The XR_007065350.1(LOC124903820):​n.2415T>C 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 0.88 in 152,214 control chromosomes in the GnomAD database, including 59,412 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 0.88 (59412 hom., cov: 34)
• Consequence: LOC124903820 XR_007065350.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.923 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.880 AC: 133823 AN: 152096 Hom.: 59369 Cov.: 34

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.990

Gnomad AMR AF: 0.897

Gnomad ASJ AF: 0.908

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.880

Gnomad FIN AF: 0.900

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.929

Gnomad OTH AF: 0.873

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

GnomAD4 genome AF: 0.880 AC: 133924 AN: 152214 Hom.: 59412 Cov.: 34 AF XY: 0.878 AC XY: 65366 AN XY: 74432

African (AFR) AF: 0.818 AC: 33968 AN: 41510

American (AMR) AF: 0.897 AC: 13734 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.908 AC: 3150 AN: 3470

East Asian (EAS) AF: 0.597 AC: 3082 AN: 5166

South Asian (SAS) AF: 0.880 AC: 4249 AN: 4828

European-Finnish (FIN) AF: 0.900 AC: 9543 AN: 10606

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.929 AC: 63176 AN: 68010

Other (OTH) AF: 0.873 AC: 1848 AN: 2116

Alfa AF: 0.893 Hom.: 3383

Bravo AF: 0.874

Asia WGS AF: 0.751 AC: 2611 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.19
DANN	Benign	0.29
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs9442384; hg19: chr1-1097287;