1-102370387-T-C

Position:

• chr1-102370387-T-C

Variant summary

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

The ENST00000447916.1(ENSG00000233359):​n.339+16818A>G 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 0.843 in 152,034 control chromosomes in the GnomAD database, including 55,951 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 0.84 (55951 hom., cov: 31)
• Consequence: ENST00000447916.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.215

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.954 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000447916.1	n.339+16818A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.843 AC: 128056 AN: 151916 Hom.: 55936 Cov.: 31

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.995

Gnomad AMR AF: 0.904

Gnomad ASJ AF: 0.946

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.907

Gnomad FIN AF: 0.970

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.942

Gnomad OTH AF: 0.867

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

GnomAD4 genome AF: 0.843 AC: 128113 AN: 152034 Hom.: 55951 Cov.: 31 AF XY: 0.847 AC XY: 62977 AN XY: 74324

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.904

Gnomad4 ASJ AF: 0.946

Gnomad4 EAS AF: 0.977

Gnomad4 SAS AF: 0.908

Gnomad4 FIN AF: 0.970

Gnomad4 NFE AF: 0.942

Gnomad4 OTH AF: 0.868

Alfa AF: 0.880 Hom.: 7097

Bravo AF: 0.824

Asia WGS AF: 0.908 AC: 3144 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.9
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10874598; hg19: chr1-102835943;