rs17160519

Variant names:

• chr7-85987149-C-A
• rs17160519
• ENST00000757672.1:n.224-20548G>T

Your query was ambiguous. Multiple possible variants found:

• chr7-85987149-C-A
• chr7-85987149-C-T

Variant summary

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

The ENST00000757672.1(ENSG00000298738):​n.224-20548G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,044 control chromosomes in the GnomAD database, including 2,678 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 0.17 (2678 hom., cov: 32)
• Consequence: ENSG00000298738 ENST00000757672.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.92
• Publications: 3 publications found

Genes affected

ENSG00000298738 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298738	ENST00000757672.1	n.224-20548G>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.171 AC: 25945 AN: 151926 Hom.: 2677 Cov.: 32

Gnomad AFR AF: 0.0533

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.171 AC: 25940 AN: 152044 Hom.: 2678 Cov.: 32 AF XY: 0.171 AC XY: 12681 AN XY: 74312

African (AFR) AF: 0.0532 AC: 2209 AN: 41530

American (AMR) AF: 0.163 AC: 2481 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 866 AN: 3464

East Asian (EAS) AF: 0.177 AC: 913 AN: 5166

South Asian (SAS) AF: 0.176 AC: 847 AN: 4818

European-Finnish (FIN) AF: 0.222 AC: 2351 AN: 10570

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.229 AC: 15578 AN: 67944

Other (OTH) AF: 0.193 AC: 407 AN: 2110

Alfa AF: 0.203 Hom.: 2711

Bravo AF: 0.164

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.0030
DANN	Benign	0.54
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs17160519; hg19: chr7-85616465;