rs1381720

Variant names:

• chr11-23394799-G-T
• rs1381720

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.15 in 152,034 control chromosomes in the GnomAD database, including 1,792 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 0.15 (1792 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.205
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.241 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: 0.150 AC: 22814 AN: 151916 Hom.: 1787 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.0703

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.0976

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.150 AC: 22831 AN: 152034 Hom.: 1792 Cov.: 32 AF XY: 0.152 AC XY: 11275 AN XY: 74336

African (AFR) AF: 0.129 AC: 5339 AN: 41468

American (AMR) AF: 0.161 AC: 2467 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0976 AC: 338 AN: 3462

East Asian (EAS) AF: 0.162 AC: 836 AN: 5162

South Asian (SAS) AF: 0.253 AC: 1217 AN: 4814

European-Finnish (FIN) AF: 0.136 AC: 1440 AN: 10580

Middle Eastern (MID) AF: 0.144 AC: 42 AN: 292

European-Non Finnish (NFE) AF: 0.159 AC: 10786 AN: 67956

Other (OTH) AF: 0.143 AC: 302 AN: 2108

Alfa AF: 0.157 Hom.: 8186

Bravo AF: 0.148

Asia WGS AF: 0.234 AC: 815 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.0
DANN	Benign	0.43
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs1381720; hg19: chr11-23416345;