rs2309717

chr4-28248616-C-Achr4-28248616-C-T

Variant summary

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

The ENST00000668598.1(ENSG00000286321):n.92+22556C>A 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 0.195 in 151,948 control chromosomes in the GnomAD database, including 3,126 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 0.19 (3126 hom., cov: 31)
• Consequence: ENST00000668598.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.761

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374557	XR_001741640.2	n.830+33468C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000668598.1	n.92+22556C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29520 AN: 151830 Hom.: 3122 Cov.: 31

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.195 AC: 29554 AN: 151948 Hom.: 3126 Cov.: 31 AF XY: 0.195 AC XY: 14464 AN XY: 74282

Gnomad4 AFR AF: 0.269

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.289

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.145

Gnomad4 OTH AF: 0.193

Alfa AF: 0.157 Hom.: 2437

Bravo AF: 0.204

Asia WGS AF: 0.208 AC: 726 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.82
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2309717; hg19: chr4-28250238;