chr10-33005847-G-A

Position:

• chr10-33005847-G-A

Variant summary

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

The NR_184020.1(ITGB1-DT):​n.270+20090G>A 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 0.106 in 152,158 control chromosomes in the GnomAD database, including 1,077 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 0.11 (1077 hom., cov: 32)
  • Exomes 𝑓: 0.048 (0 hom.)
• Consequence: ITGB1-DT NR_184020.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500

Genes affected

ITGB1-DT (HGNC:53718): (ITGB1 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ITGB1-DT	NR_184020.1	n.270+20090G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ITGB1-DT	ENST00000450890.5	n.287+20090G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16048 AN: 151998 Hom.: 1078 Cov.: 32

Gnomad AFR AF: 0.0341

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.126

GnomAD4 exome AF: 0.0476 AC: 2 AN: 42 Hom.: 0 AF XY: 0.0294 AC XY: 1 AN XY: 34

Gnomad4 AFR exome AF: 0.00

Gnomad4 NFE exome AF: 0.0556

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.106 AC: 16053 AN: 152116 Hom.: 1077 Cov.: 32 AF XY: 0.106 AC XY: 7886 AN XY: 74364

Gnomad4 AFR AF: 0.0340

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.197

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.126

Alfa AF: 0.127 Hom.: 702

Bravo AF: 0.101

Asia WGS AF: 0.171 AC: 594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.6
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11009175; hg19: chr10-33294775;