chr1-196883651-T-C

Variant names:

• chr1-196883651-T-C
• rs10801575

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 0.594 in 150,192 control chromosomes in the GnomAD database, including 29,911 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 0.59 (29911 hom., cov: 29)
• Consequence: LOC100996886 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.753
• Publications: 16 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100996886		n.196883651T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285986	ENST00000649395.1	n.427-955T>C		intron_variant	Intron 3 of 3
ENSG00000304869	ENST00000806771.1	n.221+2818T>C		intron_variant	Intron 2 of 2
ENSG00000304869	ENST00000806772.1	n.416+2818T>C		intron_variant	Intron 2 of 2
ENSG00000304869	ENST00000806773.1	n.218-3899T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.594 AC: 89114 AN: 150082 Hom.: 29892 Cov.: 29

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.830

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.633

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.594 AC: 89160 AN: 150192 Hom.: 29911 Cov.: 29 AF XY: 0.601 AC XY: 43994 AN XY: 73244

African (AFR) AF: 0.285 AC: 11615 AN: 40728

American (AMR) AF: 0.685 AC: 10264 AN: 14984

Ashkenazi Jewish (ASJ) AF: 0.633 AC: 2188 AN: 3458

East Asian (EAS) AF: 0.818 AC: 4153 AN: 5076

South Asian (SAS) AF: 0.677 AC: 3233 AN: 4776

European-Finnish (FIN) AF: 0.809 AC: 8253 AN: 10200

Middle Eastern (MID) AF: 0.524 AC: 153 AN: 292

European-Non Finnish (NFE) AF: 0.699 AC: 47304 AN: 67678

Other (OTH) AF: 0.594 AC: 1242 AN: 2090

Alfa AF: 0.675 Hom.: 33958

Bravo AF: 0.575

Asia WGS AF: 0.742 AC: 2579 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.5
DANN	Benign	0.46
PhyloP100		0.75
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: rs10801575; hg19: chr1-196852781;