chr1-196855643-T-C

Variant names:

• chr1-196855643-T-C
• rs16840639

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 0.23 in 151,340 control chromosomes in the GnomAD database, including 4,998 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 0.23 (4998 hom., cov: 32)
• Consequence: LOC100996886 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.555
• Publications: 17 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100996886		n.196855643T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285986	ENST00000649395.1	n.59-1961T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34837 AN: 151226 Hom.: 5002 Cov.: 32

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.0689

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.230 AC: 34849 AN: 151340 Hom.: 4998 Cov.: 32 AF XY: 0.230 AC XY: 16993 AN XY: 73954

African (AFR) AF: 0.341 AC: 13987 AN: 40990

American (AMR) AF: 0.170 AC: 2585 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 936 AN: 3470

East Asian (EAS) AF: 0.0689 AC: 356 AN: 5166

South Asian (SAS) AF: 0.326 AC: 1573 AN: 4824

European-Finnish (FIN) AF: 0.131 AC: 1379 AN: 10496

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.196 AC: 13293 AN: 67872

Other (OTH) AF: 0.254 AC: 534 AN: 2104

Alfa AF: 0.205 Hom.: 7019

Bravo AF: 0.234

Asia WGS AF: 0.207 AC: 721 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.61
DANN	Benign	0.35
PhyloP100		-0.56
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: rs16840639; hg19: chr1-196824773;