10-13422689-C-T

Variant names:

• chr10-13422689-C-T
• rs4748030
• ENST00000448272.1:n.56-46C>T

Variant summary

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

The ENST00000448272.1(ENSG00000286514):​n.56-46C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.929 in 152,300 control chromosomes in the GnomAD database, including 66,545 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 0.93 (66540 hom., cov: 32)
  • Exomes 𝑓: 1.0 (5 hom.)
• Consequence: ENSG00000286514 ENST00000448272.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.179
• Publications: 2 publications found

Genes affected

ENSG00000286514 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.991 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376420	NR_188196.1	n.570-46C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286514	ENST00000448272.1	n.56-46C>T		intron_variant	Intron 1 of 1	3
ENSG00000286514	ENST00000809005.1	n.250-46C>T		intron_variant	Intron 2 of 2
ENSG00000286514	ENST00000809006.1	n.258-46C>T		intron_variant	Intron 3 of 3
ENSG00000286514	ENST00000809007.1	n.170-46C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.929 AC: 141400 AN: 152172 Hom.: 66511 Cov.: 32

Gnomad AFR AF: 0.764

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.971

Gnomad ASJ AF: 0.992

Gnomad EAS AF: 0.989

Gnomad SAS AF: 0.953

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.998

Gnomad OTH AF: 0.950

GnomAD4 exome AF: 1.00 AC: 10 AN: 10 Hom.: 5 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 8 AN: 8

Other (OTH) AF: 1.00 AC: 2 AN: 2

GnomAD4 genome AF: 0.929 AC: 141481 AN: 152290 Hom.: 66540 Cov.: 32 AF XY: 0.931 AC XY: 69335 AN XY: 74464

African (AFR) AF: 0.764 AC: 31718 AN: 41504

American (AMR) AF: 0.971 AC: 14863 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.992 AC: 3443 AN: 3470

East Asian (EAS) AF: 0.989 AC: 5137 AN: 5194

South Asian (SAS) AF: 0.953 AC: 4603 AN: 4828

European-Finnish (FIN) AF: 1.00 AC: 10623 AN: 10624

Middle Eastern (MID) AF: 0.956 AC: 281 AN: 294

European-Non Finnish (NFE) AF: 0.998 AC: 67896 AN: 68048

Other (OTH) AF: 0.948 AC: 2005 AN: 2116

Alfa AF: 0.958 Hom.: 101876

Bravo AF: 0.922

Asia WGS AF: 0.952 AC: 3311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.66
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs4748030; hg19: chr10-13464689;