rs7664442

Variant names:

• chr4-23017081-A-G
• rs7664442
• ENST00000503017.2:n.332+13838A>G

Variant summary

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

The ENST00000503017.2(ENSG00000248837):​n.332+13838A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0802 in 152,116 control chromosomes in the GnomAD database, including 530 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 0.080 (530 hom., cov: 32)
• Consequence: ENSG00000248837 ENST00000503017.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.391
• Publications: 4 publications found

Genes affected

ENSG00000248837 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.088 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374524	XR_007058432.1	n.304+13838A>G		intron_variant	Intron 3 of 7
LOC105374524	XR_007058433.1	n.304+13838A>G		intron_variant	Intron 3 of 7
LOC105374524	XR_007058434.1	n.304+13838A>G		intron_variant	Intron 3 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248837	ENST00000503017.2	n.332+13838A>G		intron_variant	Intron 3 of 3	2
ENSG00000248837	ENST00000506425.2	n.304+13838A>G		intron_variant	Intron 3 of 4	3
ENSG00000248837	ENST00000511453.5	n.285+13838A>G		intron_variant	Intron 3 of 3	3

Frequencies

GnomAD3 genomes AF: 0.0802 AC: 12191 AN: 152002 Hom.: 525 Cov.: 32

Gnomad AFR AF: 0.0902

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.0546

Gnomad ASJ AF: 0.0673

Gnomad EAS AF: 0.0527

Gnomad SAS AF: 0.0406

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0768

Gnomad OTH AF: 0.0840

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

GnomAD4 genome AF: 0.0802 AC: 12206 AN: 152116 Hom.: 530 Cov.: 32 AF XY: 0.0806 AC XY: 5992 AN XY: 74376

African (AFR) AF: 0.0904 AC: 3753 AN: 41502

American (AMR) AF: 0.0545 AC: 833 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0673 AC: 233 AN: 3464

East Asian (EAS) AF: 0.0522 AC: 270 AN: 5168

South Asian (SAS) AF: 0.0402 AC: 194 AN: 4822

European-Finnish (FIN) AF: 0.128 AC: 1349 AN: 10558

Middle Eastern (MID) AF: 0.107 AC: 31 AN: 290

European-Non Finnish (NFE) AF: 0.0768 AC: 5223 AN: 67996

Other (OTH) AF: 0.0841 AC: 178 AN: 2116

Alfa AF: 0.0755 Hom.: 792

Bravo AF: 0.0771

Asia WGS AF: 0.0600 AC: 205 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.6
DANN	Benign	0.79
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs7664442; hg19: chr4-23018704;