rs17207005

Variant names:

• chr5-86143967-T-C
• rs17207005
• ENST00000837336.1:n.417A>G

Variant summary

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

The ENST00000837336.1(ENSG00000308925):​n.417A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0294 in 152,160 control chromosomes in the GnomAD database, including 84 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 0.029 (84 hom., cov: 31)
• Consequence: ENSG00000308925 ENST00000837336.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08
• Publications: 1 publications found

Genes affected

ENSG00000308925 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0294 (4466/152160) while in subpopulation NFE AF = 0.0462 (3142/67984). AF 95% confidence interval is 0.0449. There are 84 homozygotes in GnomAd4. There are 2067 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 84 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
ENSG00000308925	ENST00000837336.1	n.417A>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000308925	ENST00000837335.1	n.165-18541A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0294 AC: 4464 AN: 152044 Hom.: 83 Cov.: 31

Gnomad AFR AF: 0.00884

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0339

Gnomad ASJ AF: 0.0597

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00891

Gnomad FIN AF: 0.0106

Gnomad MID AF: 0.0318

Gnomad NFE AF: 0.0462

Gnomad OTH AF: 0.0321

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

GnomAD4 genome AF: 0.0294 AC: 4466 AN: 152160 Hom.: 84 Cov.: 31 AF XY: 0.0278 AC XY: 2067 AN XY: 74394

African (AFR) AF: 0.00886 AC: 368 AN: 41524

American (AMR) AF: 0.0339 AC: 517 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0597 AC: 207 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5172

South Asian (SAS) AF: 0.00891 AC: 43 AN: 4824

European-Finnish (FIN) AF: 0.0106 AC: 112 AN: 10610

Middle Eastern (MID) AF: 0.0308 AC: 9 AN: 292

European-Non Finnish (NFE) AF: 0.0462 AC: 3142 AN: 67984

Other (OTH) AF: 0.0318 AC: 67 AN: 2110

Alfa AF: 0.0323 Hom.: 13

Bravo AF: 0.0299

Asia WGS AF: 0.00549 AC: 20 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.43
DANN	Benign	0.40
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs17207005; hg19: chr5-85439785;