4-33964745-C-T

Position:

• chr4-33964745-C-T

Variant summary

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

The NR_125902.1(LOC101928622):​n.307+6046G>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 0.327 in 152,020 control chromosomes in the GnomAD database, including 15,460 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 0.33 (15460 hom., cov: 33)
• Consequence: LOC101928622 NR_125902.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0590

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928622	NR_125902.1	n.307+6046G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000505326.6	n.299-14995C>T		intron_variant, non_coding_transcript_variant		4
	ENST00000664054.1	n.81-17221G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49631 AN: 151904 Hom.: 15402 Cov.: 33

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.327 AC: 49749 AN: 152020 Hom.: 15460 Cov.: 33 AF XY: 0.325 AC XY: 24113 AN XY: 74294

Gnomad4 AFR AF: 0.818

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.283

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.274

Alfa AF: 0.238 Hom.: 1544

Bravo AF: 0.358

Asia WGS AF: 0.287 AC: 999 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9306906; hg19: chr4-33966367;