chr10-63898984-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000444770.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000228566	ENST00000444770.1	TSL:3	n.495-91285T>C		intron	N/A
	ENSG00000228566	ENST00000654191.1		n.407+26008T>C		intron	N/A
	ENSG00000228566	ENST00000660795.1		n.156+11896T>C		intron	N/A

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

African (AFR) AF: 0.879 AC: 36499 AN: 41516

American (AMR) AF: 0.966 AC: 14784 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.978 AC: 3397 AN: 3472

East Asian (EAS) AF: 0.934 AC: 4836 AN: 5176

South Asian (SAS) AF: 0.923 AC: 4449 AN: 4820

European-Finnish (FIN) AF: 0.958 AC: 10164 AN: 10606

Middle Eastern (MID) AF: 0.976 AC: 287 AN: 294

European-Non Finnish (NFE) AF: 0.966 AC: 65745 AN: 68034

Other (OTH) AF: 0.953 AC: 2015 AN: 2114

Alfa AF: 0.958 Hom.: 208057

Bravo AF: 0.938

Asia WGS AF: 0.931 AC: 3240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.14
DANN	Benign	0.78
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs938036; hg19: chr10-65658744;