chr17-37685518-A-G

Variant names:

• chr17-37685518-A-G
• rs11263755
• ENST00000717157.1:n.680-629A>G

Variant summary

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

The ENST00000717157.1(ENSG00000277688):​n.680-629A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 152,102 control chromosomes in the GnomAD database, including 3,261 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 0.20 (3261 hom., cov: 32)
• Consequence: ENSG00000277688 ENST00000717157.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.339
• Publications: 9 publications found

Genes affected

ENSG00000277688 (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 (EAS) allele frequency at 95% confidence interval = 0.371 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
ENSG00000277688	ENST00000717157.1	n.680-629A>G		intron_variant	Intron 4 of 4
ENSG00000277688	ENST00000717158.1	n.980+1099A>G		intron_variant	Intron 3 of 4
ENSG00000277688	ENST00000717159.1	n.306-629A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30641 AN: 151984 Hom.: 3252 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.202 AC: 30676 AN: 152102 Hom.: 3261 Cov.: 32 AF XY: 0.207 AC XY: 15426 AN XY: 74376

African (AFR) AF: 0.200 AC: 8307 AN: 41454

American (AMR) AF: 0.168 AC: 2562 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1089 AN: 3472

East Asian (EAS) AF: 0.385 AC: 1990 AN: 5170

South Asian (SAS) AF: 0.316 AC: 1521 AN: 4820

European-Finnish (FIN) AF: 0.215 AC: 2277 AN: 10588

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

European-Non Finnish (NFE) AF: 0.179 AC: 12162 AN: 67994

Other (OTH) AF: 0.224 AC: 473 AN: 2112

Alfa AF: 0.192 Hom.: 7459

Bravo AF: 0.197

Asia WGS AF: 0.344 AC: 1193 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	7.4
DANN	Benign	0.57
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs11263755; hg19: chr17-36045521;