rs73043383

Variant names:

• chr2-201103523-C-T
• rs73043383

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 0.17 in 151,892 control chromosomes in the GnomAD database, including 2,393 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 0.17 (2393 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.288
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.207 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: 0.170 AC: 25774 AN: 151774 Hom.: 2387 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.00848

Gnomad SAS AF: 0.0702

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.170 AC: 25802 AN: 151892 Hom.: 2393 Cov.: 32 AF XY: 0.167 AC XY: 12389 AN XY: 74228

African (AFR) AF: 0.211 AC: 8726 AN: 41414

American (AMR) AF: 0.144 AC: 2202 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 744 AN: 3464

East Asian (EAS) AF: 0.00850 AC: 44 AN: 5174

South Asian (SAS) AF: 0.0703 AC: 338 AN: 4808

European-Finnish (FIN) AF: 0.165 AC: 1731 AN: 10514

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11495 AN: 67964

Other (OTH) AF: 0.171 AC: 361 AN: 2106

Alfa AF: 0.175 Hom.: 316

Bravo AF: 0.172

Asia WGS AF: 0.0560 AC: 196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.3
DANN	Benign	0.51
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs73043383; hg19: chr2-201968246;