17-409857-G-A

Variant names:

• chr17-409857-G-A
• rs11150882
• ENST00000599026.1:n.175C>T

Variant summary

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

The ENST00000599026.1(ENSG00000241525):​n.175C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 153,352 control chromosomes in the GnomAD database, including 10,823 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 0.35 (10757 hom., cov: 31)
  • Exomes 𝑓: 0.26 (66 hom.)
• Consequence: ENSG00000241525 ENST00000599026.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.30
• Publications: 36 publications found

Genes affected

ENSG00000241525 (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 (AFR) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000599026.1. 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
	LOC105371430	NR_136407.1		n.330+3272C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000241525	ENST00000599026.1	TSL:5	n.175C>T		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000241525	ENST00000466740.2	TSL:3	n.330+3272C>T		intron	N/A
	ENSG00000241525	ENST00000629249.1	TSL:5	n.255+3272C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52698 AN: 151714 Hom.: 10730 Cov.: 31

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.318

GnomAD4 exome AF: 0.261 AC: 397 AN: 1520 Hom.: 66 Cov.: 0 AF XY: 0.267 AC XY: 248 AN XY: 928

African (AFR) AF: 0.531 AC: 17 AN: 32

American (AMR) AF: 0.100 AC: 1 AN: 10

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 6 AN: 28

East Asian (EAS) AF: 0.375 AC: 3 AN: 8

South Asian (SAS) AF: 0.347 AC: 209 AN: 602

European-Finnish (FIN) AF: 0.119 AC: 5 AN: 42

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.186 AC: 134 AN: 722

Other (OTH) AF: 0.284 AC: 21 AN: 74

GnomAD4 genome AF: 0.348 AC: 52783 AN: 151832 Hom.: 10757 Cov.: 31 AF XY: 0.345 AC XY: 25570 AN XY: 74218

African (AFR) AF: 0.573 AC: 23697 AN: 41362

American (AMR) AF: 0.295 AC: 4504 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1078 AN: 3466

East Asian (EAS) AF: 0.314 AC: 1617 AN: 5150

South Asian (SAS) AF: 0.355 AC: 1708 AN: 4812

European-Finnish (FIN) AF: 0.249 AC: 2623 AN: 10546

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16498 AN: 67926

Other (OTH) AF: 0.316 AC: 664 AN: 2100

Alfa AF: 0.280 Hom.: 17820

Bravo AF: 0.361

Asia WGS AF: 0.331 AC: 1153 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	1.8
DANN	Benign	0.69
PhyloP100		-2.3
PromoterAI		-0.060	Neutral

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: rs11150882;

hg19: chr17-259648;