rs2602846

Positions:

• chr4-99104000-T-A
• chr4-99104000-T-G

Variant summary

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

The NR_037884.1(LOC100507053):​n.428+14716T>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 0.789 in 152,100 control chromosomes in the GnomAD database, including 47,889 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 0.79 (47889 hom., cov: 31)
• Consequence: LOC100507053 NR_037884.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0200

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100507053	NR_037884.1	n.428+14716T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000500358.6	n.428+14716T>A		intron_variant, non_coding_transcript_variant		1
	ENST00000661393.1	n.425+14716T>A		intron_variant, non_coding_transcript_variant
	ENST00000670724.1	n.480+14716T>A		intron_variant, non_coding_transcript_variant
	ENST00000691990.1	n.446+14716T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.789 AC: 119859 AN: 151982 Hom.: 47837 Cov.: 31

Gnomad AFR AF: 0.876

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.798

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.884

Gnomad FIN AF: 0.774

Gnomad MID AF: 0.771

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.758

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

GnomAD4 genome AF: 0.789 AC: 119972 AN: 152100 Hom.: 47889 Cov.: 31 AF XY: 0.797 AC XY: 59225 AN XY: 74352

Gnomad4 AFR AF: 0.876

Gnomad4 AMR AF: 0.798

Gnomad4 ASJ AF: 0.698

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.884

Gnomad4 FIN AF: 0.774

Gnomad4 NFE AF: 0.720

Gnomad4 OTH AF: 0.761

Alfa AF: 0.755 Hom.: 5453

Bravo AF: 0.794

Asia WGS AF: 0.931 AC: 3236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.1
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2602846; hg19: chr4-100025151;