6-164384226-T-A

Variant names:

• chr6-164384226-T-A
• rs1472343
• ENST00000850290.1:n.777+46436T>A

Variant summary

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

The ENST00000850290.1(ENSG00000310478):​n.777+46436T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 151,886 control chromosomes in the GnomAD database, including 15,195 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 0.44 (15195 hom., cov: 32)
• Consequence: ENSG00000310478 ENST00000850290.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.280
• Publications: 1 publications found

Genes affected

ENSG00000310478 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000850290.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000310478	ENST00000850290.1		n.777+46436T>A		intron	N/A
	ENSG00000310478	ENST00000850291.1		n.713+46406T>A		intron	N/A
	ENSG00000310478	ENST00000850292.1		n.763-24013T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67187 AN: 151770 Hom.: 15154 Cov.: 32

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.406

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.443 AC: 67280 AN: 151886 Hom.: 15195 Cov.: 32 AF XY: 0.441 AC XY: 32739 AN XY: 74222

African (AFR) AF: 0.481 AC: 19926 AN: 41424

American (AMR) AF: 0.477 AC: 7271 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1743 AN: 3466

East Asian (EAS) AF: 0.501 AC: 2578 AN: 5146

South Asian (SAS) AF: 0.513 AC: 2471 AN: 4820

European-Finnish (FIN) AF: 0.338 AC: 3571 AN: 10550

Middle Eastern (MID) AF: 0.462 AC: 135 AN: 292

European-Non Finnish (NFE) AF: 0.416 AC: 28290 AN: 67926

Other (OTH) AF: 0.438 AC: 925 AN: 2110

Alfa AF: 0.262 Hom.: 570

Bravo AF: 0.455

Asia WGS AF: 0.551 AC: 1913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.063
DANN	Benign	0.79
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs1472343; hg19: chr6-164805259; COSMIC: COSV60300793;