1-196854170-C-T

Position:

• chr1-196854170-C-T

Variant summary

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

The ENST00000649395.1(ENSG00000285986):​n.59-3434C>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 0.194 in 151,310 control chromosomes in the GnomAD database, including 3,819 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 0.19 (3819 hom., cov: 32)
• Consequence: ENST00000649395.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.202

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.376 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
	ENST00000649395.1	n.59-3434C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29259 AN: 151194 Hom.: 3807 Cov.: 32

Gnomad AFR AF: 0.0644

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.194 AC: 29292 AN: 151310 Hom.: 3819 Cov.: 32 AF XY: 0.200 AC XY: 14769 AN XY: 73910

Gnomad4 AFR AF: 0.0645

Gnomad4 AMR AF: 0.313

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.390

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.269

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.210

Alfa AF: 0.199 Hom.: 3395

Bravo AF: 0.191

Asia WGS AF: 0.328 AC: 1136 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.33
DANN	Benign	0.14

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10922144; hg19: chr1-196823300;