chr2-71103201-C-T

Position:

• chr2-71103201-C-T

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.71103201C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;