4-99296586-C-T

Variant summary

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

The NR_037884.1(LOC100507053):n.4161-3713C>T 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 0.289 in 151,936 control chromosomes in the GnomAD database, including 7,367 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 0.29 (7367 hom., cov: 33)
• Consequence: LOC100507053 NR_037884.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100507053	NR_037884.1	n.4161-3713C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000500358.6	n.4161-3713C>T		intron_variant, non_coding_transcript_variant		1
	ENST00000509939.1	n.71-3713C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000661393.1	n.1269-3713C>T		intron_variant, non_coding_transcript_variant
	ENST00000691990.1	n.1039-3713C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43899 AN: 151818 Hom.: 7368 Cov.: 33

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.0264

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.289 AC: 43912 AN: 151936 Hom.: 7367 Cov.: 33 AF XY: 0.282 AC XY: 20931 AN XY: 74250

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.270

Gnomad4 ASJ AF: 0.452

Gnomad4 EAS AF: 0.0264

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.360

Gnomad4 NFE AF: 0.384

Gnomad4 OTH AF: 0.332

Alfa AF: 0.362 Hom.: 14019

Bravo AF: 0.277

Asia WGS AF: 0.105 AC: 367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.47
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1826909; hg19: chr4-100217743;