rs17835853

Variant names:

• chr5-51877490-G-A
• rs17835853
• ENST00000771174.1:n.917+977C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-51877490-G-A
• chr5-51877490-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000771174.1(ENSG00000300361):​n.917+977C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0296 in 152,154 control chromosomes in the GnomAD database, including 108 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 0.030 (108 hom., cov: 32)
• Consequence: ENSG00000300361 ENST00000771174.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93
• Publications: 1 publications found

Genes affected

ENSG00000300361 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0296 (4506/152154) while in subpopulation AFR AF = 0.0487 (2022/41494). AF 95% confidence interval is 0.047. There are 108 homozygotes in GnomAd4. There are 2060 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 108 gene

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
ENSG00000300361	ENST00000771174.1	n.917+977C>T		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.0296 AC: 4499 AN: 152036 Hom.: 108 Cov.: 32

Gnomad AFR AF: 0.0487

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0173

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.00415

Gnomad FIN AF: 0.00633

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0285

Gnomad OTH AF: 0.0282

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

GnomAD4 genome AF: 0.0296 AC: 4506 AN: 152154 Hom.: 108 Cov.: 32 AF XY: 0.0277 AC XY: 2060 AN XY: 74388

African (AFR) AF: 0.0487 AC: 2022 AN: 41494

American (AMR) AF: 0.0173 AC: 264 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0239 AC: 83 AN: 3472

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5166

South Asian (SAS) AF: 0.00415 AC: 20 AN: 4814

European-Finnish (FIN) AF: 0.00633 AC: 67 AN: 10586

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0285 AC: 1939 AN: 68012

Other (OTH) AF: 0.0279 AC: 59 AN: 2114

Alfa AF: 0.0277 Hom.: 135

Bravo AF: 0.0314

Asia WGS AF: 0.00520 AC: 18 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.39
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs17835853; hg19: chr5-51173324;