chr1-209091807-T-C

Variant names:

• chr1-209091807-T-C
• rs1330232
• XR_001738441.2:n.495+40947A>G

Variant summary

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

The XR_001738441.2(LOC107985255):​n.495+40947A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 152,070 control chromosomes in the GnomAD database, including 2,868 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 0.19 (2868 hom., cov: 32)
• Consequence: LOC107985255 XR_001738441.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.691
• Publications: 1 publications found

Genes affected

LOC107985255 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.256 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: 0.187 AC: 28389 AN: 151952 Hom.: 2865 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.187 AC: 28416 AN: 152070 Hom.: 2868 Cov.: 32 AF XY: 0.183 AC XY: 13622 AN XY: 74356

African (AFR) AF: 0.260 AC: 10789 AN: 41480

American (AMR) AF: 0.146 AC: 2238 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 664 AN: 3468

East Asian (EAS) AF: 0.130 AC: 675 AN: 5192

South Asian (SAS) AF: 0.112 AC: 539 AN: 4822

European-Finnish (FIN) AF: 0.150 AC: 1589 AN: 10576

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11384 AN: 67940

Other (OTH) AF: 0.175 AC: 368 AN: 2104

Alfa AF: 0.157 Hom.: 1512

Bravo AF: 0.190

Asia WGS AF: 0.137 AC: 473 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.53
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs1330232; hg19: chr1-209265152;