rs3828541

Positions:

• chr4-99121111-A-G

Variant summary

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

The NR_037884.1(LOC100507053):​n.429-12444A>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 0.387 in 152,050 control chromosomes in the GnomAD database, including 11,941 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 (11941 hom., cov: 32)
• Consequence: LOC100507053 NR_037884.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.821

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100507053	NR_037884.1	n.429-12444A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000500358.6	n.429-12444A>G		intron_variant, non_coding_transcript_variant		1
	ENST00000661393.1	n.426-12444A>G		intron_variant, non_coding_transcript_variant
	ENST00000670724.1	n.481-12444A>G		intron_variant, non_coding_transcript_variant
	ENST00000691990.1	n.446+31827A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58746 AN: 151932 Hom.: 11929 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.387 AC: 58782 AN: 152050 Hom.: 11941 Cov.: 32 AF XY: 0.387 AC XY: 28787 AN XY: 74314

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.394

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.501

Gnomad4 FIN AF: 0.463

Gnomad4 NFE AF: 0.449

Gnomad4 OTH AF: 0.389

Alfa AF: 0.428 Hom.: 22291

Bravo AF: 0.369

Asia WGS AF: 0.380 AC: 1324 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.5
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3828541; hg19: chr4-100042262;