rs10943724

Positions:

• chr6-80593088-C-A

Variant summary

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

The XR_002956360.2(LOC112267962):​n.183+12683C>A 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 0.265 in 151,976 control chromosomes in the GnomAD database, including 6,533 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 0.26 (6533 hom., cov: 32)
• Consequence: LOC112267962 XR_002956360.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99

Genes affected

LOC112267962 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC112267962	XR_002956360.2	n.183+12683C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40215 AN: 151858 Hom.: 6534 Cov.: 32

Gnomad AFR AF: 0.0896

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.265 AC: 40218 AN: 151976 Hom.: 6533 Cov.: 32 AF XY: 0.270 AC XY: 20045 AN XY: 74266

Gnomad4 AFR AF: 0.0894

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.480

Gnomad4 SAS AF: 0.448

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.322

Alfa AF: 0.305 Hom.: 4019

Bravo AF: 0.265

Asia WGS AF: 0.421 AC: 1459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.16
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10943724; hg19: chr6-81302805;