17-30244910-C-T

Variant names:

• chr17-30244910-C-T
• rs12945042
• ENST00000577420.2:n.259+6110C>T

Variant summary

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

The ENST00000577420.2(ENSG00000266120):​n.259+6110C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 151,972 control chromosomes in the GnomAD database, including 6,607 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 (6607 hom., cov: 32)
• Consequence: ENSG00000266120 ENST00000577420.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.494
• Publications: 5 publications found

Genes affected

ENSG00000266120 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000577420.2. 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
	ENSG00000266120	ENST00000577420.2	TSL:3	n.259+6110C>T		intron	N/A
	ENSG00000266120	ENST00000724730.1		n.258-4877C>T		intron	N/A
	ENSG00000266120	ENST00000724731.1		n.721-838C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43367 AN: 151854 Hom.: 6593 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.306

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.286 AC: 43415 AN: 151972 Hom.: 6607 Cov.: 32 AF XY: 0.283 AC XY: 20989 AN XY: 74262

African (AFR) AF: 0.209 AC: 8657 AN: 41430

American (AMR) AF: 0.282 AC: 4313 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 823 AN: 3466

East Asian (EAS) AF: 0.164 AC: 848 AN: 5180

South Asian (SAS) AF: 0.267 AC: 1280 AN: 4800

European-Finnish (FIN) AF: 0.362 AC: 3812 AN: 10536

Middle Eastern (MID) AF: 0.308 AC: 90 AN: 292

European-Non Finnish (NFE) AF: 0.332 AC: 22590 AN: 67978

Other (OTH) AF: 0.288 AC: 609 AN: 2112

Alfa AF: 0.237 Hom.: 925

Bravo AF: 0.275

Asia WGS AF: 0.277 AC: 964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.84
DANN	Benign	0.83
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs12945042; hg19: chr17-28571928;