rs6012418

Positions:

• chr20-48407759-G-A
• chr20-48407759-G-T

Variant summary

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

The ENST00000655426.1(ENSG00000274261):​n.628+355G>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 0.213 in 152,204 control chromosomes in the GnomAD database, including 5,318 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 0.21 (5318 hom., cov: 33)
• Consequence: ENST00000655426.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.409

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000655426.1	n.628+355G>A		intron_variant, non_coding_transcript_variant
	ENST00000615740.1	n.38+355G>A		intron_variant, non_coding_transcript_variant		5
	ENST00000665877.1	n.576+355G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32335 AN: 152086 Hom.: 5291 Cov.: 33

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.0671

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.0416

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0894

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.213 AC: 32414 AN: 152204 Hom.: 5318 Cov.: 33 AF XY: 0.217 AC XY: 16123 AN XY: 74408

Gnomad4 AFR AF: 0.422

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.0671

Gnomad4 EAS AF: 0.219

Gnomad4 SAS AF: 0.0414

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.0893

Gnomad4 OTH AF: 0.183

Alfa AF: 0.109 Hom.: 2404

Bravo AF: 0.241

Asia WGS AF: 0.167 AC: 582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.21
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6012418; hg19: chr20-47036502;