rs13103321

Positions:

• chr4-99299083-G-T

Variant summary

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

The NR_037884.1(LOC100507053):​n.4161-1216G>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 0.273 in 152,032 control chromosomes in the GnomAD database, including 6,979 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 0.27 (6979 hom., cov: 32)
• Consequence: LOC100507053 NR_037884.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100507053	NR_037884.1	n.4161-1216G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000500358.6	n.4161-1216G>T		intron_variant, non_coding_transcript_variant		1
	ENST00000509939.1	n.71-1216G>T		intron_variant, non_coding_transcript_variant		3
	ENST00000661393.1	n.1269-1216G>T		intron_variant, non_coding_transcript_variant
	ENST00000691990.1	n.1039-1216G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41471 AN: 151914 Hom.: 6984 Cov.: 32

Gnomad AFR AF: 0.0997

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.0262

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.273 AC: 41471 AN: 152032 Hom.: 6979 Cov.: 32 AF XY: 0.267 AC XY: 19839 AN XY: 74328

Gnomad4 AFR AF: 0.0997

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.450

Gnomad4 EAS AF: 0.0262

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.358

Gnomad4 NFE AF: 0.382

Gnomad4 OTH AF: 0.316

Alfa AF: 0.358 Hom.: 13227

Bravo AF: 0.258

Asia WGS AF: 0.0990 AC: 347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13103321; hg19: chr4-100220240;