rs1264202

Variant names:

• chr8-101215695-A-C
• rs1264202
• XR_928468.3:n.667+1270A>C

Your query was ambiguous. Multiple possible variants found:

• chr8-101215695-A-C
• chr8-101215695-A-G
• chr8-101215695-A-T

Variant summary

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

The XR_928468.3(LOC107984005):​n.667+1270A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.674 in 152,048 control chromosomes in the GnomAD database, including 35,438 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 0.67 (35438 hom., cov: 32)
• Consequence: LOC107984005 XR_928468.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.320
• Publications: 14 publications found

Genes affected

LOC107984005 (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 (AFR) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.674 AC: 102376 AN: 151930 Hom.: 35367 Cov.: 32

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.674 AC: 102514 AN: 152048 Hom.: 35438 Cov.: 32 AF XY: 0.674 AC XY: 50068 AN XY: 74334

African (AFR) AF: 0.836 AC: 34676 AN: 41486

American (AMR) AF: 0.694 AC: 10578 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1944 AN: 3466

East Asian (EAS) AF: 0.544 AC: 2811 AN: 5170

South Asian (SAS) AF: 0.641 AC: 3089 AN: 4818

European-Finnish (FIN) AF: 0.602 AC: 6370 AN: 10582

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.602 AC: 40945 AN: 67964

Other (OTH) AF: 0.648 AC: 1368 AN: 2110

Alfa AF: 0.620 Hom.: 102017

Bravo AF: 0.687

Asia WGS AF: 0.641 AC: 2227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.5
DANN	Benign	0.64
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs1264202; hg19: chr8-102227923;