2-71103201-C-T

Variant names:

• chr2-71103201-C-T
• rs7558220

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 0.0855 in 152,082 control chromosomes in the GnomAD database, including 678 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 0.085 (678 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 6 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 (SAS) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0853 AC: 12970 AN: 151964 Hom.: 674 Cov.: 31

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.0903

Gnomad AMR AF: 0.0989

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.0268

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0607

Gnomad OTH AF: 0.0960

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

GnomAD4 genome AF: 0.0855 AC: 13003 AN: 152082 Hom.: 678 Cov.: 31 AF XY: 0.0861 AC XY: 6403 AN XY: 74364

African (AFR) AF: 0.122 AC: 5060 AN: 41464

American (AMR) AF: 0.0989 AC: 1511 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 391 AN: 3468

East Asian (EAS) AF: 0.125 AC: 646 AN: 5154

South Asian (SAS) AF: 0.136 AC: 656 AN: 4820

European-Finnish (FIN) AF: 0.0268 AC: 284 AN: 10596

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0607 AC: 4130 AN: 68000

Other (OTH) AF: 0.102 AC: 214 AN: 2106

Alfa AF: 0.0747 Hom.: 650

Bravo AF: 0.0922

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.53
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs7558220; hg19: chr2-71330331;