5-68522754-A-G

Variant names:

• chr5-68522754-A-G
• rs7726943
• ENST00000507733.3:n.347-88277T>C

Variant summary

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

The ENST00000507733.3(ENSG00000248884):​n.347-88277T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.392 in 152,136 control chromosomes in the GnomAD database, including 11,974 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 0.39 (11974 hom., cov: 33)
• Consequence: ENSG00000248884 ENST00000507733.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146
• Publications: 6 publications found

Genes affected

ENSG00000248884 (HGNC:58096):

ENSG00000249588 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000507733.3. 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
	ENSG00000248884	ENST00000507733.3	TSL:2	n.347-88277T>C		intron	N/A
	ENSG00000248884	ENST00000663729.1		n.368+4060T>C		intron	N/A
	ENSG00000248884	ENST00000668654.2		n.380+9006T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59587 AN: 152018 Hom.: 11953 Cov.: 33

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.392 AC: 59636 AN: 152136 Hom.: 11974 Cov.: 33 AF XY: 0.393 AC XY: 29218 AN XY: 74352

African (AFR) AF: 0.404 AC: 16750 AN: 41494

American (AMR) AF: 0.324 AC: 4964 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1496 AN: 3470

East Asian (EAS) AF: 0.188 AC: 976 AN: 5184

South Asian (SAS) AF: 0.523 AC: 2519 AN: 4818

European-Finnish (FIN) AF: 0.431 AC: 4565 AN: 10580

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.398 AC: 27081 AN: 67974

Other (OTH) AF: 0.380 AC: 802 AN: 2112

Alfa AF: 0.404 Hom.: 6552

Bravo AF: 0.382

Asia WGS AF: 0.353 AC: 1229 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.6
DANN	Benign	0.49
PhyloP100		0.15

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: rs7726943;

hg19: chr5-67818581;

COSMIC: COSV72863307;