rs7603514

Variant names:

• chr2-205971888-G-A
• rs7603514

Your query was ambiguous. Multiple possible variants found:

• chr2-205971888-G-A
• chr2-205971888-G-C

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 0.186 in 152,044 control chromosomes in the GnomAD database, including 2,761 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 0.19 (2761 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.198 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: 0.186 AC: 28325 AN: 151926 Hom.: 2757 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.186 AC: 28344 AN: 152044 Hom.: 2761 Cov.: 32 AF XY: 0.183 AC XY: 13600 AN XY: 74342

African (AFR) AF: 0.186 AC: 7731 AN: 41462

American (AMR) AF: 0.151 AC: 2313 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 595 AN: 3468

East Asian (EAS) AF: 0.170 AC: 879 AN: 5156

South Asian (SAS) AF: 0.200 AC: 967 AN: 4832

European-Finnish (FIN) AF: 0.138 AC: 1463 AN: 10576

Middle Eastern (MID) AF: 0.209 AC: 61 AN: 292

European-Non Finnish (NFE) AF: 0.201 AC: 13628 AN: 67964

Other (OTH) AF: 0.198 AC: 417 AN: 2108

Alfa AF: 0.192 Hom.: 10241

Bravo AF: 0.188

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.58
DANN	Benign	0.37
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs7603514; hg19: chr2-206836612;