rs2666035

Variant names:

• chr2-54711701-T-A
• rs2666035

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 0.0784 in 152,270 control chromosomes in the GnomAD database, including 534 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 0.078 (534 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.34
• Publications: 1 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 = 0.0965 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: 0.0785 AC: 11951 AN: 152152 Hom.: 534 Cov.: 33

Gnomad AFR AF: 0.0503

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.0877

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0410

Gnomad FIN AF: 0.0777

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.0985

Gnomad OTH AF: 0.0989

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

GnomAD4 genome AF: 0.0784 AC: 11942 AN: 152270 Hom.: 534 Cov.: 33 AF XY: 0.0777 AC XY: 5783 AN XY: 74462

African (AFR) AF: 0.0502 AC: 2085 AN: 41574

American (AMR) AF: 0.0875 AC: 1339 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 417 AN: 3468

East Asian (EAS) AF: 0.000385 AC: 2 AN: 5190

South Asian (SAS) AF: 0.0410 AC: 198 AN: 4828

European-Finnish (FIN) AF: 0.0777 AC: 824 AN: 10600

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.0985 AC: 6695 AN: 67992

Other (OTH) AF: 0.0979 AC: 207 AN: 2114

Alfa AF: 0.0806 Hom.: 58

Bravo AF: 0.0780

Asia WGS AF: 0.0240 AC: 82 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.4
DANN	Benign	0.69
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs2666035; hg19: chr2-54938838;