rs1378696

Positions:

• chr6-112824464-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001744301.2(LOC107986634):​n.59+22298G>T variant causes a intron, non coding transcript 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_001744301.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

Genes affected

LOC107986634 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC107986634	XR_001744301.2	n.59+22298G>T		intron_variant, non_coding_transcript_variant
LOC107986634	XR_001744300.1	n.59+22298G>T		intron_variant, non_coding_transcript_variant
LOC107986634	XR_001744302.1	n.59+22298G>T		intron_variant, non_coding_transcript_variant
LOC107986634	XR_001744303.1	n.59+22298G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.497

Gnomad4 AMR AF: 0.823

Gnomad4 ASJ AF: 0.877

Gnomad4 EAS AF: 0.807

Gnomad4 SAS AF: 0.748

Gnomad4 FIN AF: 0.703

Gnomad4 NFE AF: 0.782

Gnomad4 OTH AF: 0.769

Alfa AF: 0.737 Hom.: 6672

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1378696; hg19: chr6-113145666;