chr2-201093478-A-G

Variant names:

• chr2-201093478-A-G
• rs10205971

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 0.169 in 151,558 control chromosomes in the GnomAD database, including 2,377 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 (2377 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25645 AN: 151444 Hom.: 2371 Cov.: 31

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.00846

Gnomad SAS AF: 0.0704

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.124

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: 0.169 AC: 25671 AN: 151558 Hom.: 2377 Cov.: 31 AF XY: 0.166 AC XY: 12322 AN XY: 74092

African (AFR) AF: 0.210 AC: 8684 AN: 41374

American (AMR) AF: 0.144 AC: 2195 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 745 AN: 3470

East Asian (EAS) AF: 0.00848 AC: 44 AN: 5186

South Asian (SAS) AF: 0.0705 AC: 340 AN: 4824

European-Finnish (FIN) AF: 0.162 AC: 1671 AN: 10296

Middle Eastern (MID) AF: 0.120 AC: 35 AN: 292

European-Non Finnish (NFE) AF: 0.169 AC: 11471 AN: 67874

Other (OTH) AF: 0.171 AC: 360 AN: 2104

Alfa AF: 0.153 Hom.: 841

Bravo AF: 0.172

Asia WGS AF: 0.0550 AC: 191 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.1
DANN	Benign	0.84
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs10205971; hg19: chr2-201958201;