chr6-33580617-G-T

Variant names:

• chr6-33580617-G-T
• rs5745568
• ENST00000612409.2:n.363-3249G>T

Variant summary

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

The ENST00000612409.2(ENSG00000293518):​n.363-3249G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,212 control chromosomes in the GnomAD database, including 3,278 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 0.19 (3278 hom., cov: 33)
• Consequence: ENSG00000293518 ENST00000612409.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0910
• Publications: 33 publications found

Genes affected

ENSG00000293518 (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 = 0.331 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000612409.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293518	ENST00000612409.2	TSL:5	n.363-3249G>T		intron	N/A
	ENSG00000293518	ENST00000738005.1		n.243-4114G>T		intron	N/A
	ENSG00000293518	ENST00000738006.1		n.236-4111G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29231 AN: 152094 Hom.: 3268 Cov.: 33

Gnomad AFR AF: 0.0956

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.192 AC: 29273 AN: 152212 Hom.: 3278 Cov.: 33 AF XY: 0.203 AC XY: 15118 AN XY: 74408

African (AFR) AF: 0.0964 AC: 4006 AN: 41560

American (AMR) AF: 0.248 AC: 3797 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 883 AN: 3468

East Asian (EAS) AF: 0.279 AC: 1447 AN: 5182

South Asian (SAS) AF: 0.345 AC: 1659 AN: 4814

European-Finnish (FIN) AF: 0.305 AC: 3226 AN: 10588

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13549 AN: 67998

Other (OTH) AF: 0.170 AC: 360 AN: 2114

Alfa AF: 0.198 Hom.: 14035

Bravo AF: 0.182

Asia WGS AF: 0.237 AC: 823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.9
DANN	Benign	0.79
PhyloP100		0.091
PromoterAI		-0.023	Neutral

Splicing

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

Other links and lift over

dbSNP: rs5745568; hg19: chr6-33548394;