chr4-89685029-A-G

Variant names:

• chr4-89685029-A-G
• rs10516842
• ENST00000612706.2:n.773A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000612706.2(ENSG00000251095):​n.773A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0556 in 152,162 control chromosomes in the GnomAD database, including 447 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 0.056 (447 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000251095 ENST00000612706.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.143
• Publications: 1 publications found

Genes affected

ENSG00000251095 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.128 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000612706.2. 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
	ENSG00000251095	ENST00000612706.2	TSL:5	n.773A>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000251095	ENST00000506864.5	TSL:4	n.472-6256A>G		intron	N/A
	ENSG00000251095	ENST00000507916.6	TSL:3	n.135-6256A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0554 AC: 8423 AN: 152046 Hom.: 438 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0259

Gnomad ASJ AF: 0.00231

Gnomad EAS AF: 0.0574

Gnomad SAS AF: 0.0311

Gnomad FIN AF: 0.0528

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0223

Gnomad OTH AF: 0.0416

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: 0.0556 AC: 8463 AN: 152162 Hom.: 447 Cov.: 32 AF XY: 0.0556 AC XY: 4138 AN XY: 74408

African (AFR) AF: 0.130 AC: 5414 AN: 41512

American (AMR) AF: 0.0258 AC: 395 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.00231 AC: 8 AN: 3470

East Asian (EAS) AF: 0.0578 AC: 298 AN: 5160

South Asian (SAS) AF: 0.0307 AC: 148 AN: 4814

European-Finnish (FIN) AF: 0.0528 AC: 560 AN: 10608

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0223 AC: 1517 AN: 67984

Other (OTH) AF: 0.0468 AC: 99 AN: 2114

Alfa AF: 0.0381 Hom.: 105

Bravo AF: 0.0577

Asia WGS AF: 0.0700 AC: 243 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.67
PhyloP100		-0.14
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10516842; hg19: chr4-90606180;