2-199575918-T-G

Variant names:

• chr2-199575918-T-G
• rs4675687

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 0.877 in 152,218 control chromosomes in the GnomAD database, including 59,958 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 0.88 (59958 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0810
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.987 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.877 AC: 133366 AN: 152100 Hom.: 59945 Cov.: 33

Gnomad AFR AF: 0.709

Gnomad AMI AF: 0.981

Gnomad AMR AF: 0.828

Gnomad ASJ AF: 0.997

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.929

Gnomad FIN AF: 0.939

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.994

Gnomad OTH AF: 0.903

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

GnomAD4 genome AF: 0.877 AC: 133424 AN: 152218 Hom.: 59958 Cov.: 33 AF XY: 0.872 AC XY: 64861 AN XY: 74424

African (AFR) AF: 0.708 AC: 29397 AN: 41508

American (AMR) AF: 0.828 AC: 12655 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.997 AC: 3462 AN: 3472

East Asian (EAS) AF: 0.536 AC: 2769 AN: 5164

South Asian (SAS) AF: 0.930 AC: 4489 AN: 4828

European-Finnish (FIN) AF: 0.939 AC: 9968 AN: 10616

Middle Eastern (MID) AF: 0.976 AC: 287 AN: 294

European-Non Finnish (NFE) AF: 0.994 AC: 67592 AN: 68022

Other (OTH) AF: 0.903 AC: 1910 AN: 2114

Alfa AF: 0.947 Hom.: 79169

Bravo AF: 0.857

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.3
DANN	Benign	0.56
PhyloP100		-0.081

Splicing

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

Other links and lift over

dbSNP: rs4675687; hg19: chr2-200440641;