7-13854651-A-G

Variant names:

• chr7-13854651-A-G
• rs1019029
• ENST00000434321.1:n.92-29T>C

Variant summary

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

The ENST00000434321.1(ENSG00000224330):​n.92-29T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 151,980 control chromosomes in the GnomAD database, including 18,184 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 0.49 (18183 hom., cov: 33)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: ENSG00000224330 ENST00000434321.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 15 publications found

Genes affected

ENSG00000224330 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.502 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
ENSG00000224330	ENST00000434321.1	n.92-29T>C		intron_variant	Intron 1 of 1	5
ENSG00000224330	ENST00000654062.1	n.573-29T>C		intron_variant	Intron 2 of 2
ENSG00000224330	ENST00000835227.1	n.184-29T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.487 AC: 74019 AN: 151862 Hom.: 18149 Cov.: 33

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.491

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

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) AF: 1.00 AC: 2 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.488 AC: 74109 AN: 151978 Hom.: 18183 Cov.: 33 AF XY: 0.490 AC XY: 36411 AN XY: 74272

African (AFR) AF: 0.508 AC: 21057 AN: 41444

American (AMR) AF: 0.475 AC: 7245 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1626 AN: 3470

East Asian (EAS) AF: 0.512 AC: 2639 AN: 5152

South Asian (SAS) AF: 0.517 AC: 2497 AN: 4826

European-Finnish (FIN) AF: 0.532 AC: 5605 AN: 10538

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.466 AC: 31710 AN: 67976

Other (OTH) AF: 0.494 AC: 1043 AN: 2110

Alfa AF: 0.468 Hom.: 31996

Bravo AF: 0.483

Asia WGS AF: 0.568 AC: 1975 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.33
DANN	Benign	0.34
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1019029; hg19: chr7-13894276;