rs2069776

Variant names:

• chr4-122450821-A-G
• rs2069776

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 0.216 in 152,156 control chromosomes in the GnomAD database, including 3,948 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 (3948 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.92
• Publications: 27 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.276 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: 0.217 AC: 32927 AN: 152038 Hom.: 3948 Cov.: 32

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.138

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: 0.216 AC: 32931 AN: 152156 Hom.: 3948 Cov.: 32 AF XY: 0.207 AC XY: 15430 AN XY: 74372

African (AFR) AF: 0.148 AC: 6129 AN: 41504

American (AMR) AF: 0.189 AC: 2888 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1032 AN: 3470

East Asian (EAS) AF: 0.138 AC: 713 AN: 5178

South Asian (SAS) AF: 0.164 AC: 792 AN: 4830

European-Finnish (FIN) AF: 0.141 AC: 1493 AN: 10602

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

European-Non Finnish (NFE) AF: 0.279 AC: 18960 AN: 67968

Other (OTH) AF: 0.231 AC: 489 AN: 2114

Alfa AF: 0.220 Hom.: 1066

Bravo AF: 0.219

Asia WGS AF: 0.166 AC: 577 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.17
DANN	Benign	0.73
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs2069776; hg19: chr4-123371976;