1-30399349-C-T

Variant names:

• chr1-30399349-C-T
• rs3907322

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 0.231 in 152,034 control chromosomes in the GnomAD database, including 4,931 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 0.23 (4931 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.614

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.389 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: 0.231 AC: 35115 AN: 151916 Hom.: 4919 Cov.: 31

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.231 AC: 35164 AN: 152034 Hom.: 4931 Cov.: 31 AF XY: 0.233 AC XY: 17327 AN XY: 74300

Gnomad4 AFR AF: 0.394

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.269

Gnomad4 SAS AF: 0.335

Gnomad4 FIN AF: 0.174

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.213

Alfa AF: 0.128 Hom.: 320

Bravo AF: 0.236

Asia WGS AF: 0.305 AC: 1058 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.054
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3907322; hg19: chr1-30872196;