7-27192143-C-T

Variant names:

• chr7-27192143-C-T
• rs4722672
• ENST00000523331.1:n.305+1001G>A

Variant summary

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

The ENST00000523331.1(ENSG00000253508):​n.305+1001G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.735 in 152,132 control chromosomes in the GnomAD database, including 42,169 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 0.74 (42169 hom., cov: 33)
• Consequence: ENSG00000253508 ENST00000523331.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.471
• Publications: 45 publications found

Genes affected

ENSG00000253508 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.814 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
ENSG00000253508	ENST00000523331.1	n.305+1001G>A		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.736 AC: 111810 AN: 152014 Hom.: 42171 Cov.: 33

Gnomad AFR AF: 0.569

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.755

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.836

Gnomad FIN AF: 0.790

Gnomad MID AF: 0.834

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.762

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

GnomAD4 genome AF: 0.735 AC: 111834 AN: 152132 Hom.: 42169 Cov.: 33 AF XY: 0.734 AC XY: 54615 AN XY: 74368

African (AFR) AF: 0.568 AC: 23551 AN: 41476

American (AMR) AF: 0.755 AC: 11551 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.882 AC: 3061 AN: 3472

East Asian (EAS) AF: 0.596 AC: 3060 AN: 5138

South Asian (SAS) AF: 0.836 AC: 4032 AN: 4824

European-Finnish (FIN) AF: 0.790 AC: 8375 AN: 10602

Middle Eastern (MID) AF: 0.832 AC: 243 AN: 292

European-Non Finnish (NFE) AF: 0.818 AC: 55602 AN: 68004

Other (OTH) AF: 0.764 AC: 1615 AN: 2114

Alfa AF: 0.772 Hom.: 84928

Bravo AF: 0.722

Asia WGS AF: 0.732 AC: 2545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	11
DANN	Benign	0.79
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs4722672; hg19: chr7-27231762;