chr6-119735680-A-G

Variant names:

• chr6-119735680-A-G
• rs6899335
• NR_134600.1:n.253-107386A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_134600.1(LOC105377975):​n.253-107386A>G variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.642
• Publications: 1 publications found

Genes affected

LOC105377975 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_134600.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105377975	NR_134600.1		n.253-107386A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.209 AC: 8663 AN: 41474

American (AMR) AF: 0.407 AC: 6200 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1314 AN: 3472

East Asian (EAS) AF: 0.562 AC: 2890 AN: 5146

South Asian (SAS) AF: 0.364 AC: 1750 AN: 4814

European-Finnish (FIN) AF: 0.301 AC: 3180 AN: 10580

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.345 AC: 23465 AN: 67950

Other (OTH) AF: 0.347 AC: 732 AN: 2110

Alfa AF: 0.331 Hom.: 1114

Bravo AF: 0.326

Asia WGS AF: 0.393 AC: 1361 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.0
DANN	Benign	0.47
PhyloP100		0.64

Splicing

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

Other links and lift over

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