4-99068108-G-A

Variant names:

• chr4-99068108-G-A
• rs1230155
• ENST00000609071.1:n.18C>T

Variant summary

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

The ENST00000609071.1(ENSG00000272777):​n.18C>T 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 0.7 in 152,004 control chromosomes in the GnomAD database, including 37,462 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 0.70 (37460 hom., cov: 31)
  • Exomes 𝑓: 0.83 (2 hom.)
• Consequence: ENSG00000272777 ENST00000609071.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.854
• Publications: 12 publications found

Genes affected

ENSG00000272777 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 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
ENSG00000272777	ENST00000609071.1	n.18C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.700 AC: 106242 AN: 151880 Hom.: 37432 Cov.: 31

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.642

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.993

Gnomad SAS AF: 0.848

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.681

GnomAD4 exome AF: 0.833 AC: 5 AN: 6 Hom.: 2 Cov.: 0 AF XY: 0.750 AC XY: 3 AN XY: 4

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 2 AN: 2

Other (OTH) AC: 0 AN: 0

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.699 AC: 106322 AN: 151998 Hom.: 37460 Cov.: 31 AF XY: 0.708 AC XY: 52634 AN XY: 74320

African (AFR) AF: 0.687 AC: 28470 AN: 41436

American (AMR) AF: 0.723 AC: 11041 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2288 AN: 3472

East Asian (EAS) AF: 0.993 AC: 5152 AN: 5186

South Asian (SAS) AF: 0.849 AC: 4091 AN: 4820

European-Finnish (FIN) AF: 0.705 AC: 7440 AN: 10550

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.671 AC: 45605 AN: 67956

Other (OTH) AF: 0.685 AC: 1439 AN: 2102

Alfa AF: 0.681 Hom.: 112611

Bravo AF: 0.698

Asia WGS AF: 0.896 AC: 3113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.3
DANN	Benign	0.81
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs1230155; hg19: chr4-99989259;