6-120074294-T-G

Variant names:

• chr6-120074294-T-G
• rs10484967
• ENST00000834274.1:n.95-54273T>G

Variant summary

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

The ENST00000834274.1(ENSG00000308468):​n.95-54273T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0731 in 151,722 control chromosomes in the GnomAD database, including 747 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 0.073 (747 hom., cov: 32)
• Consequence: ENSG00000308468 ENST00000834274.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.436
• Publications: 2 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308468	ENST00000834274.1	n.95-54273T>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.0731 AC: 11083 AN: 151604 Hom.: 745 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0390

Gnomad ASJ AF: 0.0268

Gnomad EAS AF: 0.0611

Gnomad SAS AF: 0.0389

Gnomad FIN AF: 0.00819

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0319

Gnomad OTH AF: 0.0644

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

GnomAD4 genome AF: 0.0731 AC: 11087 AN: 151722 Hom.: 747 Cov.: 32 AF XY: 0.0712 AC XY: 5281 AN XY: 74164

African (AFR) AF: 0.181 AC: 7498 AN: 41482

American (AMR) AF: 0.0390 AC: 592 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.0268 AC: 93 AN: 3464

East Asian (EAS) AF: 0.0612 AC: 316 AN: 5164

South Asian (SAS) AF: 0.0389 AC: 188 AN: 4830

European-Finnish (FIN) AF: 0.00819 AC: 87 AN: 10620

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0319 AC: 2159 AN: 67672

Other (OTH) AF: 0.0637 AC: 134 AN: 2104

Alfa AF: 0.0210 Hom.: 12

Bravo AF: 0.0794

Asia WGS AF: 0.0610 AC: 212 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.65
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs10484967; hg19: chr6-120395440;