rs1587264

chr4-99296626-G-Achr4-99296626-G-Cchr4-99296626-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.4161-3673G>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 0.771 in 152,052 control chromosomes in the GnomAD database, including 45,351 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 0.77 (45351 hom., cov: 33)
• Consequence: LOC100507053 NR_037884.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.545

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100507053	NR_037884.1	n.4161-3673G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000500358.6	n.4161-3673G>A		intron_variant, non_coding_transcript_variant		1
	ENST00000509939.1	n.71-3673G>A		intron_variant, non_coding_transcript_variant		3
	ENST00000661393.1	n.1269-3673G>A		intron_variant, non_coding_transcript_variant
	ENST00000691990.1	n.1039-3673G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.771 AC: 117211 AN: 151936 Hom.: 45313 Cov.: 33

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.805

Gnomad EAS AF: 0.910

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.788

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

GnomAD4 genome AF: 0.771 AC: 117302 AN: 152052 Hom.: 45351 Cov.: 33 AF XY: 0.768 AC XY: 57090 AN XY: 74328

Gnomad4 AFR AF: 0.726

Gnomad4 AMR AF: 0.764

Gnomad4 ASJ AF: 0.805

Gnomad4 EAS AF: 0.910

Gnomad4 SAS AF: 0.709

Gnomad4 FIN AF: 0.745

Gnomad4 NFE AF: 0.796

Gnomad4 OTH AF: 0.784

Alfa AF: 0.785 Hom.: 5819

Bravo AF: 0.771

Asia WGS AF: 0.729 AC: 2534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	2.3
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1587264; hg19: chr4-100217783;