rs1378696

Variant names:

• chr6-112824464-C-A
• rs1378696
• XR_001744300.1:n.59+22298G>T

Variant summary

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

The XR_001744300.1(LOC107986634):​n.59+22298G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.704 in 151,970 control chromosomes in the GnomAD database, including 38,945 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 0.70 (38945 hom., cov: 32)
• Consequence: LOC107986634 XR_001744300.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 1 publications found

Genes affected

LOC107986634 (HGNC:):

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 (AMR) allele frequency at 95% confidence interval = 0.811 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: 0.704 AC: 106904 AN: 151848 Hom.: 38926 Cov.: 32

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.661

Gnomad AMR AF: 0.823

Gnomad ASJ AF: 0.877

Gnomad EAS AF: 0.806

Gnomad SAS AF: 0.747

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.863

Gnomad NFE AF: 0.782

Gnomad OTH AF: 0.768

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

GnomAD4 genome AF: 0.704 AC: 106971 AN: 151970 Hom.: 38945 Cov.: 32 AF XY: 0.705 AC XY: 52399 AN XY: 74302

African (AFR) AF: 0.497 AC: 20568 AN: 41412

American (AMR) AF: 0.823 AC: 12567 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.877 AC: 3040 AN: 3466

East Asian (EAS) AF: 0.807 AC: 4149 AN: 5144

South Asian (SAS) AF: 0.748 AC: 3607 AN: 4822

European-Finnish (FIN) AF: 0.703 AC: 7443 AN: 10586

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.782 AC: 53120 AN: 67958

Other (OTH) AF: 0.769 AC: 1624 AN: 2112

Alfa AF: 0.728 Hom.: 6756

Bravo AF: 0.707

Asia WGS AF: 0.740 AC: 2566 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.23
DANN	Benign	0.51
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1378696; hg19: chr6-113145666;