rs1938684

Variant names:

• chr11-69462338-G-A
• rs1938684

Your query was ambiguous. Multiple possible variants found:

• chr11-69462338-G-A
• chr11-69462338-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 0.32 in 150,310 control chromosomes in the GnomAD database, including 10,360 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 0.32 (10360 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.676 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: 0.319 AC: 47966 AN: 150186 Hom.: 10316 Cov.: 32

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.148

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.320 AC: 48072 AN: 150310 Hom.: 10360 Cov.: 32 AF XY: 0.324 AC XY: 23781 AN XY: 73490

Gnomad4 AFR AF: 0.555

Gnomad4 AMR AF: 0.404

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.696

Gnomad4 SAS AF: 0.362

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.269

Alfa AF: 0.191 Hom.: 4997

Bravo AF: 0.341

Asia WGS AF: 0.533 AC: 1852 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.65
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1938684; hg19: chr11-69277106;