rs244040

Variant names:

• chr4-110308365-G-A
• rs244040

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 0.35 in 151,960 control chromosomes in the GnomAD database, including 9,578 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 0.35 (9578 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.605

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.377 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: 0.350 AC: 53185 AN: 151842 Hom.: 9567 Cov.: 32

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.406

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.350 AC: 53213 AN: 151960 Hom.: 9578 Cov.: 32 AF XY: 0.346 AC XY: 25713 AN XY: 74266

Gnomad4 AFR AF: 0.361

Gnomad4 AMR AF: 0.310

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.173

Gnomad4 SAS AF: 0.391

Gnomad4 FIN AF: 0.335

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.375

Alfa AF: 0.364 Hom.: 7395

Bravo AF: 0.344

Asia WGS AF: 0.303 AC: 1052 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs244040; hg19: chr4-111229521;