chr3-148697100-T-A

Position:

• chr3-148697100-T-A

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 0.2 in 152,202 control chromosomes in the GnomAD database, including 3,402 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 0.20 (3402 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.441

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.272 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: 0.200 AC: 30460 AN: 152084 Hom.: 3391 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.200 AC: 30496 AN: 152202 Hom.: 3402 Cov.: 32 AF XY: 0.197 AC XY: 14696 AN XY: 74418

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.207

Alfa AF: 0.205 Hom.: 302

Bravo AF: 0.204

Asia WGS AF: 0.131 AC: 461 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.2
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs275651; hg19: chr3-148414887;