rs16959655

Variant names:

• chr17-65087820-T-C
• rs16959655
• ENST00000759247.1:n.31+12861A>G

Your query was ambiguous. Multiple possible variants found:

• chr17-65087820-T-C
• chr17-65087820-T-G

Variant summary

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

The ENST00000759247.1(ENSG00000298947):​n.31+12861A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,132 control chromosomes in the GnomAD database, including 1,490 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 0.11 (1490 hom., cov: 32)
• Consequence: ENSG00000298947 ENST00000759247.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.476
• Publications: 4 publications found

Genes affected

ENSG00000298947 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371864	XR_007065878.1	n.193+3706A>G		intron_variant	Intron 2 of 2
LOC105371864	XR_934923.2	n.109+3706A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298947	ENST00000759247.1	n.31+12861A>G		intron_variant	Intron 1 of 1
ENSG00000298947	ENST00000759248.1	n.114+3706A>G		intron_variant	Intron 2 of 2
ENSG00000298947	ENST00000759249.1	n.35-9265A>G		intron_variant	Intron 1 of 1
ENSG00000298947	ENST00000759250.1	n.195+3706A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16849 AN: 152014 Hom.: 1484 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.0862

Gnomad EAS AF: 0.0659

Gnomad SAS AF: 0.0723

Gnomad FIN AF: 0.0365

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0465

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.111 AC: 16883 AN: 152132 Hom.: 1490 Cov.: 32 AF XY: 0.109 AC XY: 8133 AN XY: 74382

African (AFR) AF: 0.234 AC: 9700 AN: 41490

American (AMR) AF: 0.149 AC: 2282 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0862 AC: 299 AN: 3468

East Asian (EAS) AF: 0.0653 AC: 338 AN: 5180

South Asian (SAS) AF: 0.0719 AC: 346 AN: 4812

European-Finnish (FIN) AF: 0.0365 AC: 387 AN: 10590

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0465 AC: 3163 AN: 68000

Other (OTH) AF: 0.116 AC: 246 AN: 2114

Alfa AF: 0.0645 Hom.: 418

Bravo AF: 0.129

Asia WGS AF: 0.0970 AC: 338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.1
DANN	Benign	0.57
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs16959655; hg19: chr17-63083938;