4-122449894-A-G

Variant names:

• chr4-122449894-A-G
• rs11575812

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 0.217 in 152,050 control chromosomes in the GnomAD database, including 3,949 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 0.22 (3949 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293
• Publications: 19 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 (NFE) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32933 AN: 151932 Hom.: 3949 Cov.: 31

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.217 AC: 32939 AN: 152050 Hom.: 3949 Cov.: 31 AF XY: 0.208 AC XY: 15449 AN XY: 74338

African (AFR) AF: 0.148 AC: 6128 AN: 41462

American (AMR) AF: 0.189 AC: 2882 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1032 AN: 3468

East Asian (EAS) AF: 0.137 AC: 706 AN: 5166

South Asian (SAS) AF: 0.164 AC: 792 AN: 4820

European-Finnish (FIN) AF: 0.141 AC: 1495 AN: 10576

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.279 AC: 18979 AN: 67986

Other (OTH) AF: 0.232 AC: 489 AN: 2112

Alfa AF: 0.262 Hom.: 9018

Bravo AF: 0.219

Asia WGS AF: 0.167 AC: 580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.0
DANN	Benign	0.65
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs11575812; hg19: chr4-123371049;