rs11738738

Variant names:

• chr5-139332497-T-A
• rs11738738

Your query was ambiguous. Multiple possible variants found:

• chr5-139332497-T-A
• chr5-139332497-T-C
• chr5-139332497-T-G

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 0.511 in 152,046 control chromosomes in the GnomAD database, including 24,131 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 0.51 (24131 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

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 (NFE) allele frequency at 95% confidence interval = 0.692 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: 0.511 AC: 77622 AN: 151928 Hom.: 24134 Cov.: 31

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.511 AC: 77622 AN: 152046 Hom.: 24131 Cov.: 31 AF XY: 0.506 AC XY: 37604 AN XY: 74304

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.573

Gnomad4 ASJ AF: 0.689

Gnomad4 EAS AF: 0.197

Gnomad4 SAS AF: 0.621

Gnomad4 FIN AF: 0.621

Gnomad4 NFE AF: 0.697

Gnomad4 OTH AF: 0.546

Alfa AF: 0.497 Hom.: 1795

Bravo AF: 0.490

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.55
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11738738; hg19: chr5-138668186;