chr1-243852691-C-T

Variant names:

• chr1-243852691-C-T
• rs4430311

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 0.587 in 151,894 control chromosomes in the GnomAD database, including 27,295 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 0.59 (27295 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.666 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: 0.587 AC: 89092 AN: 151776 Hom.: 27273 Cov.: 31

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.757

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.587 AC: 89166 AN: 151894 Hom.: 27295 Cov.: 31 AF XY: 0.585 AC XY: 43445 AN XY: 74228

Gnomad4 AFR AF: 0.416 AC: 0.415655 AN: 0.415655

Gnomad4 AMR AF: 0.664 AC: 0.664441 AN: 0.664441

Gnomad4 ASJ AF: 0.757 AC: 0.756632 AN: 0.756632

Gnomad4 EAS AF: 0.444 AC: 0.444337 AN: 0.444337

Gnomad4 SAS AF: 0.488 AC: 0.488367 AN: 0.488367

Gnomad4 FIN AF: 0.642 AC: 0.642342 AN: 0.642342

Gnomad4 NFE AF: 0.671 AC: 0.671111 AN: 0.671111

Gnomad4 OTH AF: 0.616 AC: 0.61575 AN: 0.61575

Alfa AF: 0.644 Hom.: 130636

Bravo AF: 0.579

Asia WGS AF: 0.443 AC: 1543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4430311; hg19: chr1-244015993;