rs2697768

Variant names:

• chr2-232406207-A-C
• rs2697768

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 0.214 in 152,186 control chromosomes in the GnomAD database, including 4,315 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 0.21 (4315 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.293 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: 0.214 AC: 32506 AN: 152070 Hom.: 4310 Cov.: 32

Gnomad AFR AF: 0.0723

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.0936

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.214 AC: 32511 AN: 152186 Hom.: 4315 Cov.: 32 AF XY: 0.212 AC XY: 15744 AN XY: 74406

African (AFR) AF: 0.0725 AC: 3011 AN: 41542

American (AMR) AF: 0.203 AC: 3098 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1209 AN: 3472

East Asian (EAS) AF: 0.0934 AC: 484 AN: 5180

South Asian (SAS) AF: 0.189 AC: 908 AN: 4798

European-Finnish (FIN) AF: 0.255 AC: 2699 AN: 10600

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20128 AN: 67984

Other (OTH) AF: 0.234 AC: 495 AN: 2114

Alfa AF: 0.242 Hom.: 587

Bravo AF: 0.205

Asia WGS AF: 0.137 AC: 480 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.0
DANN	Benign	0.65
PhyloP100		-0.0040

Splicing

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

Other links and lift over

dbSNP: rs2697768; hg19: chr2-233270917;