6-119683036-G-A

Variant names:

• chr6-119683036-G-A
• rs9320700
• ENST00000701940.2:n.325-5989G>A

Variant summary

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

The ENST00000701940.2(ENSG00000287100):​n.325-5989G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 151,994 control chromosomes in the GnomAD database, including 8,076 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 0.31 (8076 hom., cov: 31)
• Consequence: ENSG00000287100 ENST00000701940.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.555
• Publications: 1 publications found

Genes affected

ENSG00000287100 (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 = 0.537 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000701940.2. 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.252+132641G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287100	ENST00000701940.2		n.325-5989G>A		intron	N/A
	ENSG00000287100	ENST00000777516.1		n.319-16305G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47466 AN: 151876 Hom.: 8067 Cov.: 31

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.313 AC: 47505 AN: 151994 Hom.: 8076 Cov.: 31 AF XY: 0.314 AC XY: 23303 AN XY: 74300

African (AFR) AF: 0.203 AC: 8407 AN: 41456

American (AMR) AF: 0.402 AC: 6139 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1269 AN: 3468

East Asian (EAS) AF: 0.554 AC: 2854 AN: 5154

South Asian (SAS) AF: 0.353 AC: 1698 AN: 4810

European-Finnish (FIN) AF: 0.289 AC: 3055 AN: 10574

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.337 AC: 22893 AN: 67956

Other (OTH) AF: 0.341 AC: 719 AN: 2110

Alfa AF: 0.322 Hom.: 1076

Bravo AF: 0.319

Asia WGS AF: 0.387 AC: 1341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.5
DANN	Benign	0.62
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs9320700; hg19: chr6-120004193; COSMIC: COSV69422700;