2-41571899-C-T

Variant names:

• chr2-41571899-C-T
• rs2217363
• XR_939997.3:n.6106G>A

Variant summary

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

The XR_939997.3(LOC105374506):​n.6106G>A 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 0.716 in 152,110 control chromosomes in the GnomAD database, including 40,053 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 0.72 (40053 hom., cov: 32)
• Consequence: LOC105374506 XR_939997.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.683
• Publications: 3 publications found

Genes affected

LOC105374506 (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 (EAS) allele frequency at 95% confidence interval = 0.932 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: 0.716 AC: 108795 AN: 151992 Hom.: 39987 Cov.: 32

Gnomad AFR AF: 0.874

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.954

Gnomad SAS AF: 0.744

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.711

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

GnomAD4 genome AF: 0.716 AC: 108924 AN: 152110 Hom.: 40053 Cov.: 32 AF XY: 0.719 AC XY: 53437 AN XY: 74342

African (AFR) AF: 0.874 AC: 36312 AN: 41526

American (AMR) AF: 0.741 AC: 11323 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.608 AC: 2112 AN: 3472

East Asian (EAS) AF: 0.954 AC: 4934 AN: 5172

South Asian (SAS) AF: 0.744 AC: 3585 AN: 4816

European-Finnish (FIN) AF: 0.626 AC: 6613 AN: 10556

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.615 AC: 41812 AN: 67970

Other (OTH) AF: 0.715 AC: 1510 AN: 2112

Alfa AF: 0.650 Hom.: 16080

Bravo AF: 0.732

Asia WGS AF: 0.853 AC: 2965 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	0.71
DANN	Benign	0.27
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs2217363; hg19: chr2-41799039;