rs856337

Positions:

• chr20-52688380-G-A
• chr20-52688380-G-C
• chr20-52688380-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000661770.1(ENSG00000232294):​n.735+215G>A 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 0.984 in 152,280 control chromosomes in the GnomAD database, including 73,782 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 0.98 (73782 hom., cov: 31)
• Consequence: ENST00000661770.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.988 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372666	XR_007067652.1	n.2021+215G>A		intron_variant, non_coding_transcript_variant
LOC105372666	XR_007067653.1	n.1347+215G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000661770.1	n.735+215G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.984 AC: 149756 AN: 152162 Hom.: 73728 Cov.: 31

Gnomad AFR AF: 0.996

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.976

Gnomad ASJ AF: 0.997

Gnomad EAS AF: 0.965

Gnomad SAS AF: 0.962

Gnomad FIN AF: 0.944

Gnomad MID AF: 0.994

Gnomad NFE AF: 0.987

Gnomad OTH AF: 0.987

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

GnomAD4 genome AF: 0.984 AC: 149867 AN: 152280 Hom.: 73782 Cov.: 31 AF XY: 0.981 AC XY: 73047 AN XY: 74454

Gnomad4 AFR AF: 0.996

Gnomad4 AMR AF: 0.975

Gnomad4 ASJ AF: 0.997

Gnomad4 EAS AF: 0.965

Gnomad4 SAS AF: 0.961

Gnomad4 FIN AF: 0.944

Gnomad4 NFE AF: 0.987

Gnomad4 OTH AF: 0.987

Alfa AF: 0.987 Hom.: 9196

Bravo AF: 0.987

Asia WGS AF: 0.960 AC: 3339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs856337; hg19: chr20-51304919;