4-99292276-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.4160+1328A>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 0.457 in 152,124 control chromosomes in the GnomAD database, including 17,766 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 0.46 (17766 hom., cov: 32)
• Consequence: LOC100507053 NR_037884.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.775 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100507053	NR_037884.1	n.4160+1328A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000500358.6	n.4160+1328A>G		intron_variant, non_coding_transcript_variant		1
	ENST00000509939.1	n.70+1271A>G		intron_variant, non_coding_transcript_variant		3
	ENST00000661393.1	n.1268+1271A>G		intron_variant, non_coding_transcript_variant
	ENST00000691990.1	n.1038+1271A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69454 AN: 152006 Hom.: 17740 Cov.: 32

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.457 AC: 69508 AN: 152124 Hom.: 17766 Cov.: 32 AF XY: 0.455 AC XY: 33837 AN XY: 74356

Gnomad4 AFR AF: 0.667

Gnomad4 AMR AF: 0.315

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.795

Gnomad4 SAS AF: 0.541

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.361

Gnomad4 OTH AF: 0.420

Alfa AF: 0.382 Hom.: 12151

Bravo AF: 0.466

Asia WGS AF: 0.544 AC: 1887 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	4.0
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1229966; hg19: chr4-100213433;