9-129430707-A-G

Variant names:

• chr9-129430707-A-G
• rs4837366
• ENST00000436510.1:n.1791T>C

Variant summary

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

The ENST00000436510.1(ENSG00000230676):​n.1791T>C 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 0.198 in 140,200 control chromosomes in the GnomAD database, including 934 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 0.20 (934 hom., cov: 45)
  • Exomes 𝑓: 0.31 (0 hom.)
• Consequence: ENSG00000230676 ENST00000436510.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178
• Publications: 1 publications found

Genes affected

ENSG00000230676 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000436510.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000230676	ENST00000436510.1	TSL:5	n.1791T>C		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000302699	ENST00000788998.1		n.934-169A>G		intron	N/A
	ENSG00000302699	ENST00000788999.1		n.308-169A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.198 AC: 27679 AN: 140068 Hom.: 931 Cov.: 45

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.210

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.223

GnomAD4 exome AF: 0.313 AC: 5 AN: 16 Hom.: 0 Cov.: 0 AF XY: 0.375 AC XY: 3 AN XY: 8

⚠️ 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) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.375 AC: 3 AN: 8

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.167 AC: 1 AN: 6

Other (OTH) AF: 0.500 AC: 1 AN: 2

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.0182349), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.198 AC: 27692 AN: 140184 Hom.: 934 Cov.: 45 AF XY: 0.201 AC XY: 13689 AN XY: 68248

African (AFR) AF: 0.102 AC: 3886 AN: 38030

American (AMR) AF: 0.304 AC: 4323 AN: 14204

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 577 AN: 3236

East Asian (EAS) AF: 0.387 AC: 1908 AN: 4932

South Asian (SAS) AF: 0.227 AC: 987 AN: 4356

European-Finnish (FIN) AF: 0.231 AC: 2221 AN: 9620

Middle Eastern (MID) AF: 0.214 AC: 56 AN: 262

European-Non Finnish (NFE) AF: 0.209 AC: 13127 AN: 62798

Other (OTH) AF: 0.225 AC: 437 AN: 1938

Alfa AF: 0.210 Hom.: 15400

Asia WGS AF: 0.324 AC: 1122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.8
DANN	Benign	0.82
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs4837366; hg19: chr9-132192986;