chr6-150541086-G-T

Variant names:

• chr6-150541086-G-T
• rs4311527
• ENST00000776319.1:n.340-25648C>A

Variant summary

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

The ENST00000776319.1(ENSG00000301114):​n.340-25648C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 152,000 control chromosomes in the GnomAD database, including 6,983 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 0.29 (6983 hom., cov: 32)
• Consequence: ENSG00000301114 ENST00000776319.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.643
• Publications: 5 publications found

Genes affected

ENSG00000301114 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.455 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
ENSG00000301114	ENST00000776319.1	n.340-25648C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43370 AN: 151882 Hom.: 6977 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.285 AC: 43388 AN: 152000 Hom.: 6983 Cov.: 32 AF XY: 0.294 AC XY: 21868 AN XY: 74268

African (AFR) AF: 0.152 AC: 6291 AN: 41508

American (AMR) AF: 0.292 AC: 4455 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1033 AN: 3470

East Asian (EAS) AF: 0.359 AC: 1849 AN: 5148

South Asian (SAS) AF: 0.472 AC: 2272 AN: 4818

European-Finnish (FIN) AF: 0.448 AC: 4719 AN: 10522

Middle Eastern (MID) AF: 0.264 AC: 77 AN: 292

European-Non Finnish (NFE) AF: 0.322 AC: 21890 AN: 67952

Other (OTH) AF: 0.251 AC: 528 AN: 2104

Alfa AF: 0.265 Hom.: 2349

Bravo AF: 0.264

Asia WGS AF: 0.373 AC: 1296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.3
DANN	Benign	0.79
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs4311527; hg19: chr6-150862222;