chr1-199936700-C-T

Position:

• chr1-199936700-C-T

Variant summary

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

The ENST00000703082.1(ENSG00000290125):​n.106-3193C>T 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 0.367 in 151,920 control chromosomes in the GnomAD database, including 12,397 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 0.37 (12397 hom., cov: 31)
• Consequence: ENST00000703082.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.745 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
	ENST00000703082.1	n.106-3193C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55746 AN: 151802 Hom.: 12389 Cov.: 31

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.423

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.367 AC: 55753 AN: 151920 Hom.: 12397 Cov.: 31 AF XY: 0.382 AC XY: 28379 AN XY: 74260

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.477

Gnomad4 ASJ AF: 0.388

Gnomad4 EAS AF: 0.765

Gnomad4 SAS AF: 0.634

Gnomad4 FIN AF: 0.512

Gnomad4 NFE AF: 0.416

Gnomad4 OTH AF: 0.371

Alfa AF: 0.407 Hom.: 7765

Bravo AF: 0.351

Asia WGS AF: 0.620 AC: 2153 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.7
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12029406; hg19: chr1-199905828;