17-78338705-G-C

Variant names:

• chr17-78338705-G-C
• rs6501199
• ENST00000586321.1:n.61-5260G>C

Variant summary

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

The ENST00000586321.1(ENSG00000267737):​n.61-5260G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.605 in 151,142 control chromosomes in the GnomAD database, including 29,093 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 0.61 (29093 hom., cov: 28)
• Consequence: ENSG00000267737 ENST00000586321.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 6 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371912	NR_188632.1	n.74-5260G>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000267737	ENST00000586321.1	n.61-5260G>C		intron_variant	Intron 1 of 2	3
ENSG00000267737	ENST00000823930.1	n.39-5260G>C		intron_variant	Intron 1 of 1
ENSG00000267737	ENST00000823931.1	n.72-5260G>C		intron_variant	Intron 1 of 1
ENSG00000307124	ENST00000823987.1	n.81-128G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.605 AC: 91404 AN: 151024 Hom.: 29085 Cov.: 28

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.608

Gnomad AMR AF: 0.681

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.731

Gnomad MID AF: 0.675

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.605 AC: 91460 AN: 151142 Hom.: 29093 Cov.: 28 AF XY: 0.608 AC XY: 44821 AN XY: 73726

African (AFR) AF: 0.389 AC: 16014 AN: 41132

American (AMR) AF: 0.681 AC: 10336 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.595 AC: 2061 AN: 3466

East Asian (EAS) AF: 0.740 AC: 3787 AN: 5120

South Asian (SAS) AF: 0.712 AC: 3410 AN: 4788

European-Finnish (FIN) AF: 0.731 AC: 7529 AN: 10294

Middle Eastern (MID) AF: 0.675 AC: 197 AN: 292

European-Non Finnish (NFE) AF: 0.682 AC: 46286 AN: 67868

Other (OTH) AF: 0.614 AC: 1290 AN: 2100

Alfa AF: 0.629 Hom.: 3873

Bravo AF: 0.591

Asia WGS AF: 0.704 AC: 2449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.33
DANN	Benign	0.39
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs6501199; hg19: chr17-76334786;