2-71103201-C-T

Variant names:

• chr2-71103201-C-T
• rs7558220

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0853 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

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.0989

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.125

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.0268

Gnomad4 NFE AF: 0.0607

Gnomad4 OTH AF: 0.102

Alfa AF: 0.0725 Hom.: 489

Bravo AF: 0.0922

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7558220; hg19: chr2-71330331;