rs1385320

Variant names:

• chr16-77508526-G-T
• rs1385320
• XR_933752.3:n.172+7452C>A

Variant summary

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

The XR_933752.3(LOC105376775):​n.172+7452C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 152,056 control chromosomes in the GnomAD database, including 11,144 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 0.38 (11144 hom., cov: 32)
• Consequence: LOC105376775 XR_933752.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.80
• Publications: 2 publications found

Genes affected

LOC105376775 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57565 AN: 151938 Hom.: 11133 Cov.: 32

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.379 AC: 57603 AN: 152056 Hom.: 11144 Cov.: 32 AF XY: 0.378 AC XY: 28118 AN XY: 74330

African (AFR) AF: 0.360 AC: 14949 AN: 41476

American (AMR) AF: 0.319 AC: 4863 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1505 AN: 3466

East Asian (EAS) AF: 0.134 AC: 692 AN: 5166

South Asian (SAS) AF: 0.427 AC: 2052 AN: 4810

European-Finnish (FIN) AF: 0.419 AC: 4434 AN: 10588

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.410 AC: 27849 AN: 67966

Other (OTH) AF: 0.352 AC: 744 AN: 2114

Alfa AF: 0.403 Hom.: 6826

Bravo AF: 0.367

Asia WGS AF: 0.316 AC: 1102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	9.7
DANN	Benign	0.76
PhyloP100		2.8

Splicing

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

Other links and lift over

dbSNP: rs1385320; hg19: chr16-77542423;