chr7-24344163-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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000662001.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000228944	ENST00000662001.2		n.203-24678A>G		intron	N/A
	ENSG00000228944	ENST00000718234.1		n.191-24678A>G		intron	N/A
	ENSG00000228944	ENST00000745512.1		n.213-24678A>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs739611;

hg19: chr7-24383782;