rs11744119

Variant names:

• chr5-40904890-G-A
• rs11744119

Your query was ambiguous. Multiple possible variants found:

• chr5-40904890-G-A
• chr5-40904890-G-C

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 0.264 in 151,950 control chromosomes in the GnomAD database, including 6,066 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 0.26 (6066 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.42 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: 0.264 AC: 40052 AN: 151830 Hom.: 6059 Cov.: 32

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.264 AC: 40082 AN: 151950 Hom.: 6066 Cov.: 32 AF XY: 0.260 AC XY: 19331 AN XY: 74296

Gnomad4 AFR AF: 0.426

Gnomad4 AMR AF: 0.208

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.196

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.262

Alfa AF: 0.202 Hom.: 5378

Bravo AF: 0.273

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	2.4
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11744119; hg19: chr5-40904992;