chr7-24213549-C-T

Variant names:

• chr7-24213549-C-T
• rs2813829
• ENST00000745616.1:n.323C>T

Variant summary

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

The ENST00000745616.1(ENSG00000297122):​n.323C>T variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 152,044 control chromosomes in the GnomAD database, including 15,527 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 0.45 (15527 hom., cov: 33)
• Consequence: ENSG00000297122 ENST00000745616.1 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.264
• Publications: 4 publications found

Genes affected

ENSG00000297122 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000745616.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297122	ENST00000745616.1		n.323C>T		splice_region non_coding_transcript_exon	Exon 2 of 4
	ENSG00000228944	ENST00000439839.1	TSL:5	n.160-16520G>A		intron	N/A
	ENSG00000228944	ENST00000718234.1		n.320-16520G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68213 AN: 151926 Hom.: 15509 Cov.: 33

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.670

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.449 AC: 68273 AN: 152044 Hom.: 15527 Cov.: 33 AF XY: 0.459 AC XY: 34103 AN XY: 74302

African (AFR) AF: 0.473 AC: 19599 AN: 41464

American (AMR) AF: 0.478 AC: 7306 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.462 AC: 1600 AN: 3466

East Asian (EAS) AF: 0.670 AC: 3455 AN: 5158

South Asian (SAS) AF: 0.523 AC: 2523 AN: 4826

European-Finnish (FIN) AF: 0.502 AC: 5310 AN: 10572

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.397 AC: 26982 AN: 67962

Other (OTH) AF: 0.466 AC: 982 AN: 2106

Alfa AF: 0.435 Hom.: 2495

Bravo AF: 0.449

Asia WGS AF: 0.574 AC: 1992 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.67
DANN	Benign	0.22
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs2813829; hg19: chr7-24253168;