rs1019102

Variant names:

• chr7-43102835-A-C
• rs1019102
• ENST00000629291.2:n.308+10789T>G

Variant summary

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

The ENST00000629291.2(ENSG00000232006):​n.308+10789T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 152,082 control chromosomes in the GnomAD database, including 10,237 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 0.36 (10237 hom., cov: 32)
• Consequence: ENSG00000232006 ENST00000629291.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.60

Genes affected

ENSG00000232006 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.448 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
ENSG00000232006	ENST00000629291.2	n.308+10789T>G		intron_variant	Intron 1 of 3	5
ENSG00000232006	ENST00000653897.1	n.296+10789T>G		intron_variant	Intron 1 of 2
ENSG00000232006	ENST00000657132.1	n.177-7671T>G		intron_variant	Intron 1 of 4
ENSG00000232006	ENST00000666102.1	n.187-7605T>G		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54663 AN: 151964 Hom.: 10231 Cov.: 32

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.360 AC: 54695 AN: 152082 Hom.: 10237 Cov.: 32 AF XY: 0.356 AC XY: 26471 AN XY: 74330

Gnomad4 AFR AF: 0.454

Gnomad4 AMR AF: 0.322

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.337

Gnomad4 OTH AF: 0.345

Alfa AF: 0.337 Hom.: 4144

Bravo AF: 0.364

Asia WGS AF: 0.282 AC: 977 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.9
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1019102; hg19: chr7-43142434;