rs1348330

Positions:

• chr4-170631706-T-C

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 0.481 in 152,110 control chromosomes in the GnomAD database, including 21,508 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 0.48 (21508 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.81 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: 0.480 AC: 73003 AN: 151994 Hom.: 21466 Cov.: 32

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.481 AC: 73100 AN: 152110 Hom.: 21508 Cov.: 32 AF XY: 0.472 AC XY: 35109 AN XY: 74374

Gnomad4 AFR AF: 0.817

Gnomad4 AMR AF: 0.552

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.157

Gnomad4 SAS AF: 0.327

Gnomad4 FIN AF: 0.211

Gnomad4 NFE AF: 0.342

Gnomad4 OTH AF: 0.472

Alfa AF: 0.433 Hom.: 2789

Bravo AF: 0.519

Asia WGS AF: 0.259 AC: 906 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.5
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1348330; hg19: chr4-171552857;