rs1448110

chr2-106787918-T-Cchr2-106787918-T-G

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 0.582 in 152,018 control chromosomes in the GnomAD database, including 26,275 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 0.58 (26275 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600

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 (EAS) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.582 AC: 88388 AN: 151900 Hom.: 26254 Cov.: 32

Gnomad AFR AF: 0.694

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.582 AC: 88455 AN: 152018 Hom.: 26275 Cov.: 32 AF XY: 0.578 AC XY: 42969 AN XY: 74298

Gnomad4 AFR AF: 0.694

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.458

Gnomad4 EAS AF: 0.695

Gnomad4 SAS AF: 0.560

Gnomad4 FIN AF: 0.530

Gnomad4 NFE AF: 0.538

Gnomad4 OTH AF: 0.534

Alfa AF: 0.559 Hom.: 3122

Bravo AF: 0.585

Asia WGS AF: 0.621 AC: 2161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.2
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1448110; hg19: chr2-107404374;