chr7-137345092-T-C

Variant names:

• chr7-137345092-T-C
• rs321198
• ENST00000438969.2:n.391A>G

Variant summary

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

The ENST00000438969.2(ENSG00000228031):​n.391A>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 0.566 in 152,122 control chromosomes in the GnomAD database, including 24,476 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 0.57 (24476 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000228031 ENST00000438969.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 21 publications found

Genes affected

ENSG00000228031 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.571 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
ENSG00000228031	ENST00000438969.2	n.391A>G		non_coding_transcript_exon_variant	Exon 4 of 4	4

Frequencies

GnomAD3 genomes AF: 0.566 AC: 86059 AN: 152004 Hom.: 24452 Cov.: 33

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.569

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: 0.566 AC: 86119 AN: 152122 Hom.: 24476 Cov.: 33 AF XY: 0.567 AC XY: 42148 AN XY: 74376

African (AFR) AF: 0.552 AC: 22876 AN: 41464

American (AMR) AF: 0.573 AC: 8764 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.612 AC: 2124 AN: 3470

East Asian (EAS) AF: 0.589 AC: 3047 AN: 5174

South Asian (SAS) AF: 0.530 AC: 2558 AN: 4824

European-Finnish (FIN) AF: 0.571 AC: 6049 AN: 10590

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.570 AC: 38754 AN: 67988

Other (OTH) AF: 0.570 AC: 1206 AN: 2114

Alfa AF: 0.568 Hom.: 37831

Bravo AF: 0.568

Asia WGS AF: 0.561 AC: 1949 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.61
DANN	Benign	0.61
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs321198; hg19: chr7-137029838;