1-61645382-A-G

Variant names:

• chr1-61645382-A-G
• rs2886326
• XR_001738095.3:n.110-2674A>G

Variant summary

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

The XR_001738095.3(LOC107984964):​n.110-2674A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.663 in 151,872 control chromosomes in the GnomAD database, including 35,305 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 0.66 (35305 hom., cov: 31)
• Consequence: LOC107984964 XR_001738095.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 6 publications found

Genes affected

LOC107984964 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.78 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: 0.663 AC: 100687 AN: 151754 Hom.: 35297 Cov.: 31

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.766

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.771

Gnomad NFE AF: 0.786

Gnomad OTH AF: 0.703

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

GnomAD4 genome AF: 0.663 AC: 100730 AN: 151872 Hom.: 35305 Cov.: 31 AF XY: 0.659 AC XY: 48942 AN XY: 74230

African (AFR) AF: 0.430 AC: 17785 AN: 41400

American (AMR) AF: 0.703 AC: 10740 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.814 AC: 2823 AN: 3470

East Asian (EAS) AF: 0.525 AC: 2706 AN: 5152

South Asian (SAS) AF: 0.768 AC: 3700 AN: 4816

European-Finnish (FIN) AF: 0.685 AC: 7193 AN: 10508

Middle Eastern (MID) AF: 0.774 AC: 226 AN: 292

European-Non Finnish (NFE) AF: 0.786 AC: 53408 AN: 67962

Other (OTH) AF: 0.701 AC: 1471 AN: 2098

Alfa AF: 0.753 Hom.: 53556

Bravo AF: 0.656

Asia WGS AF: 0.648 AC: 2252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.050
DANN	Benign	0.47
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs2886326; hg19: chr1-62111054;