rs2564978

chr1-207321071-T-C

Variant summary

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

The XR_007066838.1(LOC107985251):n.444+615A>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 0.765 in 152,128 control chromosomes in the GnomAD database, including 45,855 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 0.76 (45855 hom., cov: 32)
• Consequence: LOC107985251 XR_007066838.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0300

Genes affected

LOC107985251 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.928 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985251	XR_007066838.1	n.444+615A>G		intron_variant, non_coding_transcript_variant
LOC107985251	XR_007066837.1	n.444+615A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.765 AC: 116259 AN: 152012 Hom.: 45801 Cov.: 32

Gnomad AFR AF: 0.936

Gnomad AMI AF: 0.814

Gnomad AMR AF: 0.721

Gnomad ASJ AF: 0.869

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.781

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

GnomAD4 genome AF: 0.765 AC: 116376 AN: 152128 Hom.: 45855 Cov.: 32 AF XY: 0.759 AC XY: 56440 AN XY: 74350

Gnomad4 AFR AF: 0.936

Gnomad4 AMR AF: 0.721

Gnomad4 ASJ AF: 0.869

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.579

Gnomad4 FIN AF: 0.752

Gnomad4 NFE AF: 0.705

Gnomad4 OTH AF: 0.777

Alfa AF: 0.754 Hom.: 8557

Bravo AF: 0.772

Asia WGS AF: 0.502 AC: 1751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	6.3
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2564978; hg19: chr1-207494416;