rs1348330

Variant names:

• chr4-170631706-T-C
• rs1348330

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 0.481 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.817 AC: 33897 AN: 41500

American (AMR) AF: 0.552 AC: 8443 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1425 AN: 3470

East Asian (EAS) AF: 0.157 AC: 808 AN: 5158

South Asian (SAS) AF: 0.327 AC: 1573 AN: 4814

European-Finnish (FIN) AF: 0.211 AC: 2235 AN: 10600

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.342 AC: 23267 AN: 67972

Other (OTH) AF: 0.472 AC: 996 AN: 2110

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
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs1348330; hg19: chr4-171552857;