rs1938684

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;