rs7664442

Positions:

• chr4-23017081-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000663348.1(ENSG00000248837):​n.168+13838A>G variant causes a intron, non coding transcript 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: ENST00000663348.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.391

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105374524	XR_007058434.1	n.304+13838A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000663348.1	n.168+13838A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0904

Gnomad4 AMR AF: 0.0545

Gnomad4 ASJ AF: 0.0673

Gnomad4 EAS AF: 0.0522

Gnomad4 SAS AF: 0.0402

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.0768

Gnomad4 OTH AF: 0.0841

Alfa AF: 0.0753 Hom.: 623

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7664442; hg19: chr4-23018704;