17-67717234-G-T

Variant names:

• chr17-67717234-G-T
• rs3760220
• NR_188292.1:n.185+260C>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_188292.1(LOC101928045):​n.185+260C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.898 in 152,232 control chromosomes in the GnomAD database, including 61,430 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 0.90 (61430 hom., cov: 33)
• Consequence: LOC101928045 NR_188292.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.286

Genes affected

LOC101928045 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.933 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928045	NR_188292.1	n.185+260C>A		intron_variant	Intron 1 of 2
LOC101928045	NR_188293.1	n.37+408C>A		intron_variant	Intron 1 of 2
LOC101928045	NR_188294.1	n.37+408C>A		intron_variant	Intron 1 of 3
LOC101928045	NR_188295.1	n.185+260C>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.898 AC: 136551 AN: 152114 Hom.: 61375 Cov.: 33

Gnomad AFR AF: 0.925

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.904

Gnomad ASJ AF: 0.824

Gnomad EAS AF: 0.955

Gnomad SAS AF: 0.885

Gnomad FIN AF: 0.909

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.879

Gnomad OTH AF: 0.911

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

GnomAD4 genome AF: 0.898 AC: 136664 AN: 152232 Hom.: 61430 Cov.: 33 AF XY: 0.899 AC XY: 66909 AN XY: 74432

Gnomad4 AFR AF: 0.925

Gnomad4 AMR AF: 0.905

Gnomad4 ASJ AF: 0.824

Gnomad4 EAS AF: 0.955

Gnomad4 SAS AF: 0.885

Gnomad4 FIN AF: 0.909

Gnomad4 NFE AF: 0.879

Gnomad4 OTH AF: 0.912

Alfa AF: 0.876 Hom.: 50734

Bravo AF: 0.901

Asia WGS AF: 0.892 AC: 3101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3760220; hg19: chr17-65713350;