rs1969821

Variant names:

• chr10-87655391-G-A
• rs1969821
• ENST00000354527.2:n.146+4467C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-87655391-G-A
• chr10-87655391-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000354527.2(ENSG00000196566):​n.146+4467C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.663 in 151,878 control chromosomes in the GnomAD database, including 34,079 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 0.66 (34079 hom., cov: 31)
• Consequence: ENSG00000196566 ENST00000354527.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.853
• Publications: 3 publications found

Genes affected

ENSG00000196566 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.807 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000196566	ENST00000354527.2	n.146+4467C>T		intron_variant	Intron 1 of 3	3
ENSG00000225913	ENST00000438082.1	n.109-3112G>A		intron_variant	Intron 2 of 3	3
ENSG00000225913	ENST00000804457.1	n.370+214G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.662 AC: 100538 AN: 151760 Hom.: 34020 Cov.: 31

Gnomad AFR AF: 0.814

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.669

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.663 AC: 100655 AN: 151878 Hom.: 34079 Cov.: 31 AF XY: 0.658 AC XY: 48825 AN XY: 74208

African (AFR) AF: 0.814 AC: 33772 AN: 41470

American (AMR) AF: 0.686 AC: 10470 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.595 AC: 2064 AN: 3468

East Asian (EAS) AF: 0.553 AC: 2841 AN: 5140

South Asian (SAS) AF: 0.616 AC: 2964 AN: 4814

European-Finnish (FIN) AF: 0.569 AC: 5989 AN: 10532

Middle Eastern (MID) AF: 0.658 AC: 192 AN: 292

European-Non Finnish (NFE) AF: 0.597 AC: 40524 AN: 67882

Other (OTH) AF: 0.649 AC: 1365 AN: 2102

Alfa AF: 0.624 Hom.: 3802

Bravo AF: 0.679

Asia WGS AF: 0.605 AC: 2106 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	1.2
DANN	Benign	0.66
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs1969821; hg19: chr10-89415148;