1-209072514-T-G

Variant names:

• chr1-209072514-T-G
• rs10494916
• XR_001738441.2:n.495+60240A>C

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+60240A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 152,078 control chromosomes in the GnomAD database, including 11,663 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 0.38 (11663 hom., cov: 33)
• Consequence: LOC107985255 XR_001738441.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400
• Publications: 9 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.711 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: 0.382 AC: 58070 AN: 151956 Hom.: 11661 Cov.: 33

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.730

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.382 AC: 58095 AN: 152078 Hom.: 11663 Cov.: 33 AF XY: 0.387 AC XY: 28766 AN XY: 74328

African (AFR) AF: 0.333 AC: 13829 AN: 41484

American (AMR) AF: 0.441 AC: 6740 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1053 AN: 3468

East Asian (EAS) AF: 0.731 AC: 3777 AN: 5168

South Asian (SAS) AF: 0.310 AC: 1491 AN: 4816

European-Finnish (FIN) AF: 0.453 AC: 4794 AN: 10572

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.370 AC: 25168 AN: 67976

Other (OTH) AF: 0.371 AC: 784 AN: 2112

Alfa AF: 0.374 Hom.: 43002

Bravo AF: 0.384

Asia WGS AF: 0.504 AC: 1753 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.2
DANN	Benign	0.84
PhyloP100		0.0040

Splicing

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

Other links and lift over

dbSNP: rs10494916; hg19: chr1-209245859;