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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984005	XR_928468.3	n.667+1270A>C		intron_variant	Intron 1 of 4
LOC107984005	XR_928469.2	n.667+1270A>C		intron_variant	Intron 1 of 4

Ensembl

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

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 v4.3

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;