rs1898300

Positions:

• chr3-21200164-T-C
• chr3-21200164-T-G

Variant summary

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

The ENST00000634947.1(ENSG00000282987):​n.370+24524A>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 0.519 in 151,222 control chromosomes in the GnomAD database, including 22,363 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 0.52 (22363 hom., cov: 31)
• Consequence: ENST00000634947.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376988	XR_940646.3	n.545-10834T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000634947.1	n.370+24524A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.518 AC: 78324 AN: 151102 Hom.: 22324 Cov.: 31

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.850

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.519 AC: 78426 AN: 151222 Hom.: 22363 Cov.: 31 AF XY: 0.529 AC XY: 39117 AN XY: 73924

Gnomad4 AFR AF: 0.706

Gnomad4 AMR AF: 0.586

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.850

Gnomad4 SAS AF: 0.685

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.498

Alfa AF: 0.466 Hom.: 2993

Bravo AF: 0.537

Asia WGS AF: 0.761 AC: 2601 AN: 3420

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.97
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1898300; hg19: chr3-21241656;