1-30106075-C-T

Position:

• chr1-30106075-C-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 0.468 in 152,042 control chromosomes in the GnomAD database, including 17,429 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 0.47 (17429 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.831

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.745 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71074 AN: 151924 Hom.: 17422 Cov.: 33

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.468 AC: 71111 AN: 152042 Hom.: 17429 Cov.: 33 AF XY: 0.473 AC XY: 35157 AN XY: 74308

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.475

Gnomad4 ASJ AF: 0.568

Gnomad4 EAS AF: 0.765

Gnomad4 SAS AF: 0.574

Gnomad4 FIN AF: 0.525

Gnomad4 NFE AF: 0.503

Gnomad4 OTH AF: 0.490

Alfa AF: 0.500 Hom.: 19018

Bravo AF: 0.462

Asia WGS AF: 0.629 AC: 2190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.0
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10915029; hg19: chr1-30578922; COSMIC: COSV59935055;