chr2-41219469-T-G

Variant names:

• chr2-41219469-T-G
• rs7567386

Variant summary

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

The variant allele was found at a frequency of 0.701 in 151,990 control chromosomes in the GnomAD database, including 37,663 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 0.70 (37663 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.75 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: 0.701 AC: 106536 AN: 151870 Hom.: 37644 Cov.: 32

Gnomad AFR AF: 0.757

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.777

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.699

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

GnomAD4 genome AF: 0.701 AC: 106608 AN: 151990 Hom.: 37663 Cov.: 32 AF XY: 0.702 AC XY: 52124 AN XY: 74298

African (AFR) AF: 0.757 AC: 31365 AN: 41452

American (AMR) AF: 0.644 AC: 9818 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.777 AC: 2695 AN: 3468

East Asian (EAS) AF: 0.531 AC: 2736 AN: 5154

South Asian (SAS) AF: 0.767 AC: 3696 AN: 4820

European-Finnish (FIN) AF: 0.725 AC: 7670 AN: 10582

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.683 AC: 46401 AN: 67956

Other (OTH) AF: 0.696 AC: 1463 AN: 2102

Alfa AF: 0.687 Hom.: 153373

Bravo AF: 0.693

Asia WGS AF: 0.643 AC: 2236 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.65
DANN	Benign	0.51
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs7567386; hg19: chr2-41446609;