2-203706103-G-A

Variant names:

• chr2-203706103-G-A
• rs35593994

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 0.345 in 150,864 control chromosomes in the GnomAD database, including 9,169 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 0.35 (9169 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140
• Publications: 5 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 (SAS) allele frequency at 95% confidence interval = 0.586 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: 0.345 AC: 52071 AN: 150746 Hom.: 9170 Cov.: 28

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.345 AC: 52077 AN: 150864 Hom.: 9169 Cov.: 28 AF XY: 0.346 AC XY: 25488 AN XY: 73658

African (AFR) AF: 0.323 AC: 13243 AN: 40956

American (AMR) AF: 0.325 AC: 4918 AN: 15144

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1328 AN: 3464

East Asian (EAS) AF: 0.281 AC: 1436 AN: 5116

South Asian (SAS) AF: 0.604 AC: 2873 AN: 4754

European-Finnish (FIN) AF: 0.336 AC: 3484 AN: 10380

Middle Eastern (MID) AF: 0.445 AC: 129 AN: 290

European-Non Finnish (NFE) AF: 0.351 AC: 23773 AN: 67770

Other (OTH) AF: 0.336 AC: 699 AN: 2080

Alfa AF: 0.339 Hom.: 1099

Bravo AF: 0.338

Asia WGS AF: 0.451 AC: 1568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.42
PhyloP100		0.014
PromoterAI		0.011	Neutral

Splicing

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

Other links and lift over

dbSNP: rs35593994; hg19: chr2-204570826;