rs1264202

chr8-101215695-A-Cchr8-101215695-A-T

Variant summary

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

The XR_928468.3(LOC107984005):n.667+1270A>C 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 0.674 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.320

Genes affected

LOC107984005 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC107984005	XR_928468.3	n.667+1270A>C		intron_variant, non_coding_transcript_variant
LOC107984005	XR_928469.2	n.667+1270A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.836

Gnomad4 AMR AF: 0.694

Gnomad4 ASJ AF: 0.561

Gnomad4 EAS AF: 0.544

Gnomad4 SAS AF: 0.641

Gnomad4 FIN AF: 0.602

Gnomad4 NFE AF: 0.602

Gnomad4 OTH AF: 0.648

Alfa AF: 0.604 Hom.: 63273

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1264202; hg19: chr8-102227923;