rs10484212

Positions:

• chr4-37109858-A-T

Variant summary

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

The ENST00000671043.1(ENSG00000247810):​n.332+502A>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 0.275 in 151,968 control chromosomes in the GnomAD database, including 9,003 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 0.28 (9003 hom., cov: 32)
• Consequence: ENST00000671043.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.673

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928721	XR_427512.5	n.666+502A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000671043.1	n.332+502A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41748 AN: 151850 Hom.: 8975 Cov.: 32

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.0893

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.275 AC: 41850 AN: 151968 Hom.: 9003 Cov.: 32 AF XY: 0.275 AC XY: 20424 AN XY: 74312

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.395

Gnomad4 SAS AF: 0.0902

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.246

Alfa AF: 0.203 Hom.: 692

Bravo AF: 0.308

Asia WGS AF: 0.260 AC: 903 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.0
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484212; hg19: chr4-37111480;