7-23554431-C-T

Variant names:

• chr7-23554431-C-T
• rs6949019
• ENST00000725513.1:n.188-9091C>T

Variant summary

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

The ENST00000725513.1(ENSG00000294729):​n.188-9091C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 148,106 control chromosomes in the GnomAD database, including 20,938 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 0.53 (20938 hom., cov: 25)
• Consequence: ENSG00000294729 ENST00000725513.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 6 publications found

Genes affected

ENSG00000294729 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.619 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
ENSG00000294729	ENST00000725513.1	n.188-9091C>T		intron_variant	Intron 1 of 3
ENSG00000294729	ENST00000725514.1	n.188-9091C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.528 AC: 78132 AN: 147994 Hom.: 20907 Cov.: 25

Gnomad AFR AF: 0.625

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.550

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.542

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.528 AC: 78220 AN: 148106 Hom.: 20938 Cov.: 25 AF XY: 0.521 AC XY: 37458 AN XY: 71930

African (AFR) AF: 0.625 AC: 24911 AN: 39826

American (AMR) AF: 0.495 AC: 7253 AN: 14662

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1653 AN: 3454

East Asian (EAS) AF: 0.406 AC: 2052 AN: 5056

South Asian (SAS) AF: 0.399 AC: 1888 AN: 4728

European-Finnish (FIN) AF: 0.442 AC: 4237 AN: 9592

Middle Eastern (MID) AF: 0.543 AC: 153 AN: 282

European-Non Finnish (NFE) AF: 0.513 AC: 34640 AN: 67548

Other (OTH) AF: 0.542 AC: 1116 AN: 2058

Alfa AF: 0.501 Hom.: 2673

Bravo AF: 0.536

Asia WGS AF: 0.396 AC: 1381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.18
DANN	Benign	0.44
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs6949019; hg19: chr7-23594050;