chr2-49819714-A-G

Variant names:

• chr2-49819714-A-G
• rs17795388

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 0.121 in 152,244 control chromosomes in the GnomAD database, including 1,258 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 0.12 (1258 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00900
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.148 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: 0.121 AC: 18362 AN: 152128 Hom.: 1257 Cov.: 32

Gnomad AFR AF: 0.0920

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0685

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.121 AC: 18359 AN: 152244 Hom.: 1258 Cov.: 32 AF XY: 0.118 AC XY: 8765 AN XY: 74442

African (AFR) AF: 0.0919 AC: 3818 AN: 41562

American (AMR) AF: 0.114 AC: 1743 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 553 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5190

South Asian (SAS) AF: 0.0678 AC: 327 AN: 4826

European-Finnish (FIN) AF: 0.122 AC: 1295 AN: 10584

Middle Eastern (MID) AF: 0.137 AC: 40 AN: 292

European-Non Finnish (NFE) AF: 0.150 AC: 10197 AN: 68008

Other (OTH) AF: 0.128 AC: 270 AN: 2116

Alfa AF: 0.131 Hom.: 171

Bravo AF: 0.117

Asia WGS AF: 0.0400 AC: 139 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.6
DANN	Benign	0.66
PhyloP100		-0.0090

Splicing

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

Other links and lift over

dbSNP: rs17795388; hg19: chr2-50046852;