rs6012418

Variant names:

• chr20-48407759-G-A
• rs6012418
• ENST00000615740.1:n.38+355G>A

Your query was ambiguous. Multiple possible variants found:

• 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 ENST00000615740.1(ENSG00000274261):​n.38+355G>A variant causes a intron 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: ENSG00000274261 ENST00000615740.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.409

Genes affected

ENSG00000274261 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000274261	ENST00000615740.1	n.38+355G>A		intron_variant	Intron 1 of 2	5
ENSG00000274261	ENST00000655426.1	n.628+355G>A		intron_variant	Intron 1 of 2
ENSG00000274261	ENST00000665877.1	n.576+355G>A		intron_variant	Intron 1 of 2

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;