1-102317816-T-C

Position:

• chr1-102317816-T-C

Variant summary

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

The variant allele was found at a frequency of 0.948 in 151,786 control chromosomes in the GnomAD database, including 68,459 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 0.95 (68459 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.285

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.986 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.102317816T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000233359	ENST00000447916.1	n.340-7488A>G		intron_variant		3
ENSG00000233359	ENST00000656454.1	n.45-7488A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.948 AC: 143718 AN: 151666 Hom.: 68406 Cov.: 32

Gnomad AFR AF: 0.877

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.963

Gnomad ASJ AF: 0.991

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.923

Gnomad FIN AF: 0.999

Gnomad MID AF: 0.991

Gnomad NFE AF: 0.992

Gnomad OTH AF: 0.957

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

GnomAD4 genome AF: 0.948 AC: 143831 AN: 151786 Hom.: 68459 Cov.: 32 AF XY: 0.947 AC XY: 70219 AN XY: 74164

Gnomad4 AFR AF: 0.877

Gnomad4 AMR AF: 0.963

Gnomad4 ASJ AF: 0.991

Gnomad4 EAS AF: 0.757

Gnomad4 SAS AF: 0.922

Gnomad4 FIN AF: 0.999

Gnomad4 NFE AF: 0.992

Gnomad4 OTH AF: 0.957

Alfa AF: 0.980 Hom.: 3991

Bravo AF: 0.939

Asia WGS AF: 0.844 AC: 2930 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.7
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1935268; hg19: chr1-102783372;