6-33606636-A-G

Variant names:

• chr6-33606636-A-G
• rs210120
• ENST00000838175.1:n.200+1127T>C

Variant summary

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

The ENST00000838175.1(ENSG00000309063):​n.200+1127T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 151,946 control chromosomes in the GnomAD database, including 19,356 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 0.49 (19356 hom., cov: 31)
• Consequence: ENSG00000309063 ENST00000838175.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.331
• Publications: 17 publications found

Genes affected

ENSG00000309063 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.623 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
ENSG00000309063	ENST00000838175.1	n.200+1127T>C		intron_variant	Intron 2 of 3
ENSG00000309063	ENST00000838176.1	n.216-1076T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.494 AC: 75051 AN: 151828 Hom.: 19327 Cov.: 31

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.494 AC: 75129 AN: 151946 Hom.: 19356 Cov.: 31 AF XY: 0.489 AC XY: 36315 AN XY: 74254

African (AFR) AF: 0.629 AC: 26053 AN: 41426

American (AMR) AF: 0.456 AC: 6964 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.473 AC: 1640 AN: 3468

East Asian (EAS) AF: 0.612 AC: 3165 AN: 5168

South Asian (SAS) AF: 0.518 AC: 2496 AN: 4814

European-Finnish (FIN) AF: 0.324 AC: 3423 AN: 10556

Middle Eastern (MID) AF: 0.524 AC: 153 AN: 292

European-Non Finnish (NFE) AF: 0.439 AC: 29826 AN: 67936

Other (OTH) AF: 0.512 AC: 1079 AN: 2108

Alfa AF: 0.460 Hom.: 79336

Bravo AF: 0.506

Asia WGS AF: 0.590 AC: 2053 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.48
DANN	Benign	0.60
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs210120; hg19: chr6-33574413;