chr17-78328187-G-T

Variant names:

• chr17-78328187-G-T
• rs4436839
• ENST00000586321.1:n.60+12399G>T

Variant summary

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

The ENST00000586321.1(ENSG00000267737):​n.60+12399G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.432 in 152,116 control chromosomes in the GnomAD database, including 14,995 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 0.43 (14995 hom., cov: 33)
• Consequence: ENSG00000267737 ENST00000586321.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.48
• Publications: 4 publications found

Genes affected

ENSG00000267737 (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 (EAS) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371912	NR_188632.1	n.73+12399G>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000267737	ENST00000586321.1	n.60+12399G>T		intron_variant	Intron 1 of 2	3
ENSG00000267737	ENST00000823930.1	n.38+12399G>T		intron_variant	Intron 1 of 1
ENSG00000267737	ENST00000823931.1	n.71+10199G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65708 AN: 151998 Hom.: 14985 Cov.: 33

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.432 AC: 65753 AN: 152116 Hom.: 14995 Cov.: 33 AF XY: 0.437 AC XY: 32480 AN XY: 74350

African (AFR) AF: 0.291 AC: 12091 AN: 41506

American (AMR) AF: 0.516 AC: 7896 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1314 AN: 3470

East Asian (EAS) AF: 0.632 AC: 3271 AN: 5172

South Asian (SAS) AF: 0.503 AC: 2426 AN: 4824

European-Finnish (FIN) AF: 0.502 AC: 5308 AN: 10578

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.470 AC: 31973 AN: 67962

Other (OTH) AF: 0.454 AC: 958 AN: 2110

Alfa AF: 0.447 Hom.: 25341

Bravo AF: 0.428

Asia WGS AF: 0.565 AC: 1960 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	1.1
DANN	Benign	0.40
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs4436839; hg19: chr17-76324268;