6-120190068-G-A

Variant names:

• chr6-120190068-G-A
• rs261759
• ENST00000834274.1:n.170-10133G>A

Variant summary

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

The ENST00000834274.1(ENSG00000308468):​n.170-10133G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 152,050 control chromosomes in the GnomAD database, including 2,342 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 0.14 (2342 hom., cov: 31)
• Consequence: ENSG00000308468 ENST00000834274.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.20
• Publications: 1 publications found

Genes affected

ENSG00000308468 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000834274.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308468	ENST00000834274.1		n.170-10133G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20634 AN: 151930 Hom.: 2334 Cov.: 31

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.0627

Gnomad ASJ AF: 0.0585

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0829

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0577

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.136 AC: 20683 AN: 152050 Hom.: 2342 Cov.: 31 AF XY: 0.137 AC XY: 10161 AN XY: 74342

African (AFR) AF: 0.305 AC: 12652 AN: 41426

American (AMR) AF: 0.0625 AC: 955 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0585 AC: 203 AN: 3472

East Asian (EAS) AF: 0.213 AC: 1101 AN: 5158

South Asian (SAS) AF: 0.123 AC: 591 AN: 4822

European-Finnish (FIN) AF: 0.0829 AC: 878 AN: 10588

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0577 AC: 3925 AN: 67994

Other (OTH) AF: 0.114 AC: 241 AN: 2108

Alfa AF: 0.0473 Hom.: 85

Bravo AF: 0.141

Asia WGS AF: 0.179 AC: 620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0030
DANN	Benign	0.44
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs261759; hg19: chr6-120511214;