rs10221112

Positions:

• chr16-59085701-A-G
• chr16-59085701-A-T

Variant summary

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

The ENST00000657379.1(ENSG00000245768):​n.720+21450A>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 0.322 in 151,614 control chromosomes in the GnomAD database, including 8,062 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 0.32 (8062 hom., cov: 31)
• Consequence: ENST00000657379.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.448

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.335 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
	ENST00000657379.1	n.720+21450A>G		intron_variant, non_coding_transcript_variant
	ENST00000500117.1	n.749+21450A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48780 AN: 151496 Hom.: 8054 Cov.: 31

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.322 AC: 48823 AN: 151614 Hom.: 8062 Cov.: 31 AF XY: 0.322 AC XY: 23807 AN XY: 74042

Gnomad4 AFR AF: 0.311

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.375

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.412

Gnomad4 NFE AF: 0.338

Gnomad4 OTH AF: 0.311

Alfa AF: 0.330 Hom.: 3753

Bravo AF: 0.312

Asia WGS AF: 0.224 AC: 778 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10221112; hg19: chr16-59119605;