6-119735680-A-G

Position:

• chr6-119735680-A-G

Variant summary

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

The NR_134600.1(LOC105377975):​n.253-107386A>G 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 0.32 in 151,972 control chromosomes in the GnomAD database, including 8,431 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 0.32 (8431 hom., cov: 32)
• Consequence: LOC105377975 NR_134600.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.642

Genes affected

LOC105377975 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377975	NR_134600.1	n.253-107386A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48628 AN: 151854 Hom.: 8421 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.320 AC: 48668 AN: 151972 Hom.: 8431 Cov.: 32 AF XY: 0.321 AC XY: 23857 AN XY: 74280

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.562

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.301

Gnomad4 NFE AF: 0.345

Gnomad4 OTH AF: 0.347

Alfa AF: 0.335 Hom.: 1094

Bravo AF: 0.326

Asia WGS AF: 0.393 AC: 1361 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.0
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6899335; hg19: chr6-120056818; COSMIC: COSV69422766;