1-196854170-C-T

Variant names:

• chr1-196854170-C-T
• rs10922144

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: LOC100996886 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.202
• Publications: 13 publications found

Genes affected

LOC100996886 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC100996886		n.196854170C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285986	ENST00000649395.1	n.59-3434C>T		intron_variant	Intron 1 of 3

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

African (AFR) AF: 0.0645 AC: 2648 AN: 41084

American (AMR) AF: 0.313 AC: 4755 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 885 AN: 3462

East Asian (EAS) AF: 0.390 AC: 2008 AN: 5144

South Asian (SAS) AF: 0.248 AC: 1195 AN: 4816

European-Finnish (FIN) AF: 0.269 AC: 2805 AN: 10430

Middle Eastern (MID) AF: 0.0925 AC: 27 AN: 292

European-Non Finnish (NFE) AF: 0.212 AC: 14404 AN: 67882

Other (OTH) AF: 0.210 AC: 440 AN: 2100

Alfa AF: 0.196 Hom.: 6552

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
PhyloP100		0.20
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10922144; hg19: chr1-196823300;