rs17808497

chr20-7125573-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000425900.1(ENSG00000232271):n.82-20784A>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0355 in 152,200 control chromosomes in the GnomAD database, including 122 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 0.035 (122 hom., cov: 31)
• Consequence: ENST00000425900.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.292

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0355 (5400/152200) while in subpopulation NFE AF= 0.0424 (2885/68008). AF 95% confidence interval is 0.0411. There are 122 homozygotes in gnomad4. There are 2618 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 122 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000425900.1	n.82-20784A>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0354 AC: 5390 AN: 152082 Hom.: 122 Cov.: 31

Gnomad AFR AF: 0.0241

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0292

Gnomad ASJ AF: 0.0802

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00724

Gnomad FIN AF: 0.0540

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0424

Gnomad OTH AF: 0.0498

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

GnomAD4 genome AF: 0.0355 AC: 5400 AN: 152200 Hom.: 122 Cov.: 31 AF XY: 0.0352 AC XY: 2618 AN XY: 74432

Gnomad4 AFR AF: 0.0243

Gnomad4 AMR AF: 0.0291

Gnomad4 ASJ AF: 0.0802

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00704

Gnomad4 FIN AF: 0.0540

Gnomad4 NFE AF: 0.0424

Gnomad4 OTH AF: 0.0498

Alfa AF: 0.0389 Hom.: 21

Bravo AF: 0.0340

Asia WGS AF: 0.00866 AC: 30 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	2.4
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17808497; hg19: chr20-7106220;