chr7-24398341-C-A

Variant names:

• chr7-24398341-C-A
• rs105
• ENST00000745766.1:n.672C>A

Variant summary

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

The ENST00000745766.1(ENSG00000297140):​n.672C>A 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 0.383 in 151,810 control chromosomes in the GnomAD database, including 11,769 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 0.38 (11769 hom., cov: 31)
• Consequence: ENSG00000297140 ENST00000745766.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 6 publications found

Genes affected

ENSG00000297140 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.478 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986777	XR_001745121.2	n.80+46718G>T		intron_variant	Intron 1 of 2
LOC107986777	XR_001745122.2	n.80+46718G>T		intron_variant	Intron 1 of 1
LOC107986777	XR_001745123.2	n.80+46718G>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297140	ENST00000745766.1	n.672C>A		non_coding_transcript_exon_variant	Exon 2 of 3
ENSG00000228944	ENST00000662001.2	n.202+46718G>T		intron_variant	Intron 1 of 1
ENSG00000228944	ENST00000718234.1	n.190+46718G>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58114 AN: 151692 Hom.: 11761 Cov.: 31

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.383 AC: 58143 AN: 151810 Hom.: 11769 Cov.: 31 AF XY: 0.384 AC XY: 28451 AN XY: 74172

African (AFR) AF: 0.247 AC: 10236 AN: 41406

American (AMR) AF: 0.373 AC: 5685 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1342 AN: 3470

East Asian (EAS) AF: 0.429 AC: 2211 AN: 5156

South Asian (SAS) AF: 0.495 AC: 2372 AN: 4796

European-Finnish (FIN) AF: 0.450 AC: 4731 AN: 10504

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.445 AC: 30240 AN: 67900

Other (OTH) AF: 0.352 AC: 744 AN: 2112

Alfa AF: 0.411 Hom.: 1617

Bravo AF: 0.369

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.6
DANN	Benign	0.70
PhyloP100		0.055

Splicing

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

Other links and lift over

dbSNP: rs105; hg19: chr7-24437960;