rs10510257

Positions:

• chr3-3304454-G-A
• chr3-3304454-G-T

Variant summary

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

The ENST00000420000.6(ENSG00000223727):​n.537+32846C>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 0.222 in 151,896 control chromosomes in the GnomAD database, including 3,848 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 0.22 (3848 hom., cov: 32)
• Consequence: ENST00000420000.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.324

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000420000.6	n.537+32846C>T		intron_variant, non_coding_transcript_variant		4
	ENST00000451031.5	n.339+32846C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33673 AN: 151780 Hom.: 3840 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.222 AC: 33700 AN: 151896 Hom.: 3848 Cov.: 32 AF XY: 0.221 AC XY: 16404 AN XY: 74192

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.233

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.239

Alfa AF: 0.219 Hom.: 2566

Bravo AF: 0.223

Asia WGS AF: 0.200 AC: 698 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10510257; hg19: chr3-3346138;