rs2411738

Variant names:

• chr1-4266308-G-A
• rs2411738

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 0.399 in 152,074 control chromosomes in the GnomAD database, including 13,877 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 0.40 (13877 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.53

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.499 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: 0.399 AC: 60569 AN: 151956 Hom.: 13870 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.399 AC: 60602 AN: 152074 Hom.: 13877 Cov.: 32 AF XY: 0.400 AC XY: 29737 AN XY: 74348

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.451

Gnomad4 EAS AF: 0.226

Gnomad4 SAS AF: 0.505

Gnomad4 FIN AF: 0.490

Gnomad4 NFE AF: 0.504

Gnomad4 OTH AF: 0.397

Alfa AF: 0.467 Hom.: 9176

Bravo AF: 0.384

Asia WGS AF: 0.408 AC: 1419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.27
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2411738; hg19: chr1-4326368;