17-78315910-T-G

Variant names:

• chr17-78315910-T-G
• rs4789580
• ENST00000586321.1:n.60+122T>G

Variant summary

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

The ENST00000586321.1(ENSG00000267737):​n.60+122T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 152,582 control chromosomes in the GnomAD database, including 5,217 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 0.23 (5203 hom., cov: 32)
  • Exomes 𝑓: 0.21 (14 hom.)
• Consequence: ENSG00000267737 ENST00000586321.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 11 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000586321.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105371912	NR_188632.1		n.73+122T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000267737	ENST00000586321.1	TSL:3	n.60+122T>G		intron	N/A
	ENSG00000267737	ENST00000823930.1		n.38+122T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35495 AN: 151910 Hom.: 5201 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.242

GnomAD4 exome AF: 0.215 AC: 119 AN: 554 Hom.: 14 AF XY: 0.206 AC XY: 73 AN XY: 354

African (AFR) AF: 0.0625 AC: 1 AN: 16

American (AMR) AF: 0.250 AC: 1 AN: 4

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AF: 0.583 AC: 7 AN: 12

South Asian (SAS) AF: 0.100 AC: 2 AN: 20

European-Finnish (FIN) AF: 0.298 AC: 25 AN: 84

Middle Eastern (MID) AF: 0.333 AC: 2 AN: 6

European-Non Finnish (NFE) AF: 0.184 AC: 67 AN: 364

Other (OTH) AF: 0.283 AC: 13 AN: 46

GnomAD4 genome AF: 0.234 AC: 35502 AN: 152028 Hom.: 5203 Cov.: 32 AF XY: 0.242 AC XY: 17962 AN XY: 74310

African (AFR) AF: 0.129 AC: 5364 AN: 41480

American (AMR) AF: 0.322 AC: 4918 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 994 AN: 3468

East Asian (EAS) AF: 0.672 AC: 3453 AN: 5138

South Asian (SAS) AF: 0.407 AC: 1959 AN: 4818

European-Finnish (FIN) AF: 0.251 AC: 2658 AN: 10576

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15276 AN: 67948

Other (OTH) AF: 0.245 AC: 517 AN: 2114

Alfa AF: 0.232 Hom.: 11826

Bravo AF: 0.235

Asia WGS AF: 0.495 AC: 1717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.5
DANN	Benign	0.59
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs4789580; hg19: chr17-76311991;