2-106787918-T-C

Variant names:

• chr2-106787918-T-C
• rs1448110

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 0.582 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
• Publications: 3 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 (EAS) allele frequency at 95% confidence interval = 0.687 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: 0.582 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

African (AFR) AF: 0.694 AC: 28789 AN: 41488

American (AMR) AF: 0.507 AC: 7746 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1590 AN: 3468

East Asian (EAS) AF: 0.695 AC: 3578 AN: 5146

South Asian (SAS) AF: 0.560 AC: 2697 AN: 4814

European-Finnish (FIN) AF: 0.530 AC: 5592 AN: 10558

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.538 AC: 36568 AN: 67938

Other (OTH) AF: 0.534 AC: 1127 AN: 2112

Alfa AF: 0.563 Hom.: 3303

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
PhyloP100		0.0060

Splicing

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

Other links and lift over

dbSNP: rs1448110; hg19: chr2-107404374;