rs981579

Positions:

• chr4-28543605-A-G

Variant summary

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

The ENST00000509416.1(ENSG00000250064):​n.403-34311A>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 0.24 in 151,962 control chromosomes in the GnomAD database, including 5,369 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 0.24 (5369 hom., cov: 32)
• Consequence: ENST00000509416.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104

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 = 0.538 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374557	XR_001741640.2	n.891-34311A>G		intron_variant, non_coding_transcript_variant
LOC105374558	XR_925528.3	n.332-20449T>C		intron_variant, non_coding_transcript_variant
LOC105374557	XR_001741639.2	n.301-34311A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000509416.1	n.403-34311A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36494 AN: 151844 Hom.: 5360 Cov.: 32

Gnomad AFR AF: 0.0784

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.240 AC: 36521 AN: 151962 Hom.: 5369 Cov.: 32 AF XY: 0.244 AC XY: 18092 AN XY: 74264

Gnomad4 AFR AF: 0.0784

Gnomad4 AMR AF: 0.358

Gnomad4 ASJ AF: 0.331

Gnomad4 EAS AF: 0.555

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.264

Alfa AF: 0.266 Hom.: 1048

Bravo AF: 0.241

Asia WGS AF: 0.470 AC: 1629 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.1
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs981579; hg19: chr4-28545227;