rs2886326

Positions:

• chr1-61645382-A-G
• chr1-61645382-A-T

Variant summary

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

The XR_001738095.3(LOC107984964):​n.110-2674A>G 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 0.663 in 151,872 control chromosomes in the GnomAD database, including 35,305 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 0.66 (35305 hom., cov: 31)
• Consequence: LOC107984964 XR_001738095.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95

Genes affected

LOC107984964 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984964	XR_001738095.3	n.110-2674A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.663 AC: 100687 AN: 151754 Hom.: 35297 Cov.: 31

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.766

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.771

Gnomad NFE AF: 0.786

Gnomad OTH AF: 0.703

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

GnomAD4 genome AF: 0.663 AC: 100730 AN: 151872 Hom.: 35305 Cov.: 31 AF XY: 0.659 AC XY: 48942 AN XY: 74230

Gnomad4 AFR AF: 0.430

Gnomad4 AMR AF: 0.703

Gnomad4 ASJ AF: 0.814

Gnomad4 EAS AF: 0.525

Gnomad4 SAS AF: 0.768

Gnomad4 FIN AF: 0.685

Gnomad4 NFE AF: 0.786

Gnomad4 OTH AF: 0.701

Alfa AF: 0.752 Hom.: 30176

Bravo AF: 0.656

Asia WGS AF: 0.648 AC: 2252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.050
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2886326; hg19: chr1-62111054;