6-33570025-C-A

Variant names:

• chr6-33570025-C-A
• rs17627049
• ENST00000612409.2:n.200-738C>A

Variant summary

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

The ENST00000612409.2(ENSG00000293518):​n.200-738C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 151,914 control chromosomes in the GnomAD database, including 3,714 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 0.21 (3714 hom., cov: 30)
• Consequence: ENSG00000293518 ENST00000612409.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460
• Publications: 16 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=-0.66).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.257 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

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
	ENSG00000293518	ENST00000612409.2	TSL:5	n.200-738C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31731 AN: 151796 Hom.: 3713 Cov.: 30

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.0652

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.209 AC: 31750 AN: 151914 Hom.: 3714 Cov.: 30 AF XY: 0.200 AC XY: 14858 AN XY: 74260

African (AFR) AF: 0.160 AC: 6645 AN: 41408

American (AMR) AF: 0.203 AC: 3090 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 955 AN: 3468

East Asian (EAS) AF: 0.0651 AC: 337 AN: 5176

South Asian (SAS) AF: 0.115 AC: 553 AN: 4816

European-Finnish (FIN) AF: 0.165 AC: 1744 AN: 10564

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.260 AC: 17691 AN: 67952

Other (OTH) AF: 0.219 AC: 462 AN: 2108

Alfa AF: 0.246 Hom.: 6300

Bravo AF: 0.213

Asia WGS AF: 0.113 AC: 394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	5.4
DANN	Benign	0.89
PhyloP100		-0.046

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17627049;

hg19: chr6-33537802;