rs1620921

Positions:

• chr6-160776055-A-G

Variant summary

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

The ENST00000619095.1(ENSG00000274903):​n.45+2023A>G 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 0.6 in 152,014 control chromosomes in the GnomAD database, including 28,031 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 0.60 (28031 hom., cov: 32)
• Consequence: ENST00000619095.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.348

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.959 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000619095.1	n.45+2023A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.600 AC: 91146 AN: 151896 Hom.: 28000 Cov.: 32

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.982

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.600 AC: 91227 AN: 152014 Hom.: 28031 Cov.: 32 AF XY: 0.607 AC XY: 45092 AN XY: 74280

Gnomad4 AFR AF: 0.637

Gnomad4 AMR AF: 0.687

Gnomad4 ASJ AF: 0.506

Gnomad4 EAS AF: 0.982

Gnomad4 SAS AF: 0.716

Gnomad4 FIN AF: 0.533

Gnomad4 NFE AF: 0.536

Gnomad4 OTH AF: 0.626

Alfa AF: 0.601 Hom.: 4288

Bravo AF: 0.613

Asia WGS AF: 0.834 AC: 2894 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1620921; hg19: chr6-161197087;