rs2074136

Variant names:

• chr7-118003214-T-C
• rs2074136
• ENST00000427030.1:n.106A>G

Variant summary

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

The ENST00000427030.1(ENSG00000234826):​n.106A>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 0.115 in 152,160 control chromosomes in the GnomAD database, including 2,577 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 0.12 (2577 hom., cov: 32)
  • Exomes 𝑓: 0.029 (0 hom.)
• Consequence: ENSG00000234826 ENST00000427030.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.263
• Publications: 0 publications found

Genes affected

ENSG00000234826 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.361 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
ENSG00000234826	ENST00000427030.1	n.106A>G		non_coding_transcript_exon_variant	Exon 2 of 3	5

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17490 AN: 151976 Hom.: 2571 Cov.: 32

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0666

Gnomad ASJ AF: 0.0144

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.0674

Gnomad FIN AF: 0.00988

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0110

Gnomad OTH AF: 0.100

GnomAD4 exome AF: 0.0294 AC: 2 AN: 68 Hom.: 0 Cov.: 0 AF XY: 0.0400 AC XY: 2 AN XY: 50

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

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.0172 AC: 1 AN: 58

Other (OTH) AF: 0.00 AC: 0 AN: 2

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.115 AC: 17514 AN: 152092 Hom.: 2577 Cov.: 32 AF XY: 0.114 AC XY: 8503 AN XY: 74372

African (AFR) AF: 0.316 AC: 13106 AN: 41432

American (AMR) AF: 0.0667 AC: 1019 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0144 AC: 50 AN: 3472

East Asian (EAS) AF: 0.375 AC: 1928 AN: 5144

South Asian (SAS) AF: 0.0672 AC: 324 AN: 4820

European-Finnish (FIN) AF: 0.00988 AC: 105 AN: 10624

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0110 AC: 748 AN: 68024

Other (OTH) AF: 0.101 AC: 213 AN: 2104

Alfa AF: 0.0489 Hom.: 3859

Bravo AF: 0.131

Asia WGS AF: 0.211 AC: 732 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.1
DANN	Benign	0.60
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs2074136; hg19: chr7-117643268;