rs4513829

Positions:

• chr6-58438253-A-G
• chr6-58438253-A-T

Variant summary

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

The ENST00000641775.1(ENSG00000225096):​n.1612A>G variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.0971 in 151,496 control chromosomes in the GnomAD database, including 962 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 0.097 (962 hom., cov: 34)
  • Failed GnomAD Quality Control
• Consequence: ENST00000641775.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.247 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
	ENST00000641775.1	n.1612A>G		non_coding_transcript_exon_variant	6/6

Frequencies

GnomAD3 genomes AF: 0.0971 AC: 14692 AN: 151378 Hom.: 956 Cov.: 34

Gnomad AFR AF: 0.0273

Gnomad AMI AF: 0.0747

Gnomad AMR AF: 0.0966

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.106

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.0971 AC: 14706 AN: 151496 Hom.: 962 Cov.: 34 AF XY: 0.101 AC XY: 7465 AN XY: 73996

Gnomad4 AFR AF: 0.0272

Gnomad4 AMR AF: 0.0971

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.109

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.111

Alfa AF: 0.0965 Hom.: 92

Bravo AF: 0.0930

Asia WGS AF: 0.269 AC: 936 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.9
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4513829; hg19: chr6-58764531;