rs1448901

Positions:

• chr2-206388916-A-G
• chr2-206388916-A-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 0.207 in 152,208 control chromosomes in the GnomAD database, including 3,680 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 0.21 (3680 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.361

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31497 AN: 152090 Hom.: 3677 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.207 AC: 31514 AN: 152208 Hom.: 3680 Cov.: 32 AF XY: 0.205 AC XY: 15249 AN XY: 74416

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.222

Alfa AF: 0.241 Hom.: 1354

Bravo AF: 0.200

Asia WGS AF: 0.245 AC: 850 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	9.7
DANN	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1448901; hg19: chr2-207253640;