chr1-102648125-T-C

Variant names:

• chr1-102648125-T-C
• rs977155
• XR_947651.2:n.159-100A>G

Variant summary

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

The XR_947651.2(LOC105378874):​n.159-100A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.497 in 151,996 control chromosomes in the GnomAD database, including 20,854 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 0.50 (20854 hom., cov: 32)
• Consequence: LOC105378874 XR_947651.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.462
• Publications: 3 publications found

Genes affected

LOC105378874 (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 (AMR) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378874	XR_947651.2	n.159-100A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.497 AC: 75483 AN: 151878 Hom.: 20838 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.497 AC: 75511 AN: 151996 Hom.: 20854 Cov.: 32 AF XY: 0.506 AC XY: 37548 AN XY: 74274

African (AFR) AF: 0.237 AC: 9837 AN: 41494

American (AMR) AF: 0.624 AC: 9521 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.506 AC: 1756 AN: 3472

East Asian (EAS) AF: 0.604 AC: 3110 AN: 5152

South Asian (SAS) AF: 0.557 AC: 2686 AN: 4818

European-Finnish (FIN) AF: 0.703 AC: 7421 AN: 10554

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.580 AC: 39439 AN: 67940

Other (OTH) AF: 0.501 AC: 1058 AN: 2112

Alfa AF: 0.408 Hom.: 1274

Bravo AF: 0.483

Asia WGS AF: 0.582 AC: 2020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.48
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs977155; hg19: chr1-103113681;