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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986634	XR_001744300.1	n.59+22298G>T		intron_variant	Intron 1 of 6
LOC107986634	XR_001744301.2	n.59+22298G>T		intron_variant	Intron 1 of 5
LOC107986634	XR_001744302.1	n.59+22298G>T		intron_variant	Intron 1 of 6
LOC107986634	XR_001744303.1	n.59+22298G>T		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;