rs937091

Positions:

• chr6-119873770-C-A
• chr6-119873770-C-G

Variant summary

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

The XR_007059730.1(LOC124901390):​n.6421C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 151,460 control chromosomes in the GnomAD database, including 18,637 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 0.49 (18637 hom., cov: 31)
• Consequence: LOC124901390 XR_007059730.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.863

Genes affected

LOC124901390 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901390	XR_007059730.1	n.6421C>A		non_coding_transcript_exon_variant	1/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74046 AN: 151342 Hom.: 18630 Cov.: 31

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.489 AC: 74091 AN: 151460 Hom.: 18637 Cov.: 31 AF XY: 0.486 AC XY: 35967 AN XY: 73966

Gnomad4 AFR AF: 0.596

Gnomad4 AMR AF: 0.368

Gnomad4 ASJ AF: 0.445

Gnomad4 EAS AF: 0.635

Gnomad4 SAS AF: 0.436

Gnomad4 FIN AF: 0.497

Gnomad4 NFE AF: 0.447

Gnomad4 OTH AF: 0.471

Alfa AF: 0.455 Hom.: 7153

Bravo AF: 0.489

Asia WGS AF: 0.496 AC: 1723 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.28
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs937091; hg19: chr6-120194916;