7-24344163-T-C

Variant names:

• chr7-24344163-T-C
• rs739611
• ENST00000662001.2:n.203-24678A>G

Variant summary

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

The ENST00000662001.2(ENSG00000228944):​n.203-24678A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,102 control chromosomes in the GnomAD database, including 2,361 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 0.15 (2361 hom., cov: 32)
• Consequence: ENSG00000228944 ENST00000662001.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.731
• Publications: 2 publications found

Genes affected

ENSG00000228944 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986777	XR_001745121.2	n.81-24678A>G		intron_variant	Intron 1 of 2
LOC107986777	XR_001745122.2	n.80+100896A>G		intron_variant	Intron 1 of 1
LOC107986777	XR_001745123.2	n.81-24678A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228944	ENST00000662001.2	n.203-24678A>G		intron_variant	Intron 1 of 1
ENSG00000228944	ENST00000718234.1	n.191-24678A>G		intron_variant	Intron 1 of 3
ENSG00000228944	ENST00000745512.1	n.213-24678A>G		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23358 AN: 151986 Hom.: 2354 Cov.: 32

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.0821

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0766

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.154 AC: 23412 AN: 152102 Hom.: 2361 Cov.: 32 AF XY: 0.158 AC XY: 11762 AN XY: 74392

African (AFR) AF: 0.251 AC: 10409 AN: 41454

American (AMR) AF: 0.238 AC: 3641 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0821 AC: 285 AN: 3470

East Asian (EAS) AF: 0.316 AC: 1633 AN: 5170

South Asian (SAS) AF: 0.169 AC: 816 AN: 4822

European-Finnish (FIN) AF: 0.103 AC: 1091 AN: 10598

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0766 AC: 5209 AN: 67986

Other (OTH) AF: 0.143 AC: 302 AN: 2110

Alfa AF: 0.0926 Hom.: 1510

Bravo AF: 0.168

Asia WGS AF: 0.236 AC: 821 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.48
DANN	Benign	0.63
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs739611; hg19: chr7-24383782;