chr6-58438253-A-G

Variant names:

• chr6-58438253-A-G
• rs4513829
• ENST00000641775.1:n.1612A>G

Variant summary

Our verdict is Benign. The variant received -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: ENSG00000225096 ENST00000641775.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 2 publications found

Genes affected

ENSG00000225096 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000641775.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000225096	ENST00000641775.1		n.1612A>G		non_coding_transcript_exon	Exon 6 of 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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.0272 AC: 1127 AN: 41440

American (AMR) AF: 0.0971 AC: 1467 AN: 15110

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 456 AN: 3456

East Asian (EAS) AF: 0.259 AC: 1331 AN: 5140

South Asian (SAS) AF: 0.203 AC: 975 AN: 4814

European-Finnish (FIN) AF: 0.109 AC: 1161 AN: 10612

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7855 AN: 67614

Other (OTH) AF: 0.111 AC: 234 AN: 2106

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 v4.9

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

Other links and lift over

dbSNP: rs4513829; hg19: chr6-58764531;