chr10-63898984-T-C

Variant names:

• chr10-63898984-T-C
• rs938036
• ENST00000444770.1:n.495-91285T>C

Variant summary

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

The ENST00000444770.1(ENSG00000228566):​n.495-91285T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.939 in 152,246 control chromosomes in the GnomAD database, including 67,271 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 0.94 (67271 hom., cov: 32)
• Consequence: ENSG00000228566 ENST00000444770.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.97

Genes affected

ENSG00000228566 (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 (NFE) allele frequency at 95% confidence interval = 0.96 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902439	XR_007062159.1	n.386+11308T>C		intron_variant	Intron 1 of 2
LOC124902439	XR_007062160.1	n.386+11308T>C		intron_variant	Intron 1 of 5
LOC124902439	XR_007062161.1	n.388+26008T>C		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228566	ENST00000444770.1	n.495-91285T>C		intron_variant	Intron 2 of 2	3
ENSG00000228566	ENST00000654191.1	n.407+26008T>C		intron_variant	Intron 1 of 5
ENSG00000228566	ENST00000660795.1	n.156+11896T>C		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.939 AC: 142888 AN: 152128 Hom.: 67229 Cov.: 32

Gnomad AFR AF: 0.879

Gnomad AMI AF: 0.888

Gnomad AMR AF: 0.966

Gnomad ASJ AF: 0.978

Gnomad EAS AF: 0.934

Gnomad SAS AF: 0.923

Gnomad FIN AF: 0.958

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.966

Gnomad OTH AF: 0.953

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

GnomAD4 genome AF: 0.939 AC: 142986 AN: 152246 Hom.: 67271 Cov.: 32 AF XY: 0.938 AC XY: 69796 AN XY: 74426

Gnomad4 AFR AF: 0.879

Gnomad4 AMR AF: 0.966

Gnomad4 ASJ AF: 0.978

Gnomad4 EAS AF: 0.934

Gnomad4 SAS AF: 0.923

Gnomad4 FIN AF: 0.958

Gnomad4 NFE AF: 0.966

Gnomad4 OTH AF: 0.953

Alfa AF: 0.963 Hom.: 91134

Bravo AF: 0.938

Asia WGS AF: 0.931 AC: 3240 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	0.14
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs938036; hg19: chr10-65658744;