chr2-100727176-A-G

Variant names:

• chr2-100727176-A-G
• rs1567804
• XR_001739612.2:n.2416-2820T>C

Variant summary

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

The XR_001739612.2(LOC105375310):​n.2416-2820T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.549 in 152,114 control chromosomes in the GnomAD database, including 25,287 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 0.55 (25287 hom., cov: 33)
• Consequence: LOC105375310 XR_001739612.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.353
• Publications: 9 publications found

Genes affected

LOC105375310 (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 = 0.677 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: 0.549 AC: 83446 AN: 151996 Hom.: 25289 Cov.: 33

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.684

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.777

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.549 AC: 83457 AN: 152114 Hom.: 25287 Cov.: 33 AF XY: 0.546 AC XY: 40576 AN XY: 74368

African (AFR) AF: 0.329 AC: 13651 AN: 41476

American (AMR) AF: 0.487 AC: 7445 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.684 AC: 2372 AN: 3470

East Asian (EAS) AF: 0.304 AC: 1572 AN: 5164

South Asian (SAS) AF: 0.414 AC: 1995 AN: 4814

European-Finnish (FIN) AF: 0.777 AC: 8231 AN: 10590

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.683 AC: 46415 AN: 68006

Other (OTH) AF: 0.555 AC: 1172 AN: 2112

Alfa AF: 0.639 Hom.: 88702

Bravo AF: 0.520

Asia WGS AF: 0.330 AC: 1147 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	1.7
DANN	Benign	0.66
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs1567804; hg19: chr2-101343638;