chr2-149505610-A-G

Variant names:

• chr2-149505610-A-G
• rs7370927

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

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 0.47 (1756 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 2 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).

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: 0.471 AC: 68262 AN: 144878 Hom.: 1751 Cov.: 31

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.474

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.471

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff AF: 0.471 AC: 68300 AN: 144982 Hom.: 1756 Cov.: 31 AF XY: 0.470 AC XY: 33162 AN XY: 70536

African (AFR) AF: 0.440 AC: 17060 AN: 38794

American (AMR) AF: 0.463 AC: 6671 AN: 14414

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1641 AN: 3380

East Asian (EAS) AF: 0.495 AC: 2479 AN: 5012

South Asian (SAS) AF: 0.472 AC: 2162 AN: 4576

European-Finnish (FIN) AF: 0.496 AC: 4916 AN: 9912

Middle Eastern (MID) AF: 0.472 AC: 135 AN: 286

European-Non Finnish (NFE) AF: 0.485 AC: 31871 AN: 65744

Other (OTH) AF: 0.473 AC: 935 AN: 1978

Alfa AF: 0.407 Hom.: 41

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.12
PhyloP100		-1.5

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7370927;

hg19: chr2-150362124;

COSMIC: COSV65473380;