rs67807996

Positions:

• chr1-150023307-G-A

Variant summary

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

The XR_007066598.1(LOC124904413):​n.63+10782G>A 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 0.279 in 152,042 control chromosomes in the GnomAD database, including 7,284 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 0.28 (7284 hom., cov: 32)
• Consequence: LOC124904413 XR_007066598.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67

Genes affected

LOC124904413 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124904413	XR_007066598.1	n.63+10782G>A		intron_variant, non_coding_transcript_variant
OTUD7B	XM_047425712.1	c.-67+43651C>T		intron_variant			XP_047281668.1
OTUD7B	XM_047425716.1	c.-67+44176C>T		intron_variant			XP_047281672.1
OTUD7B	XM_047425721.1	c.-67+44176C>T		intron_variant			XP_047281677.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42452 AN: 151924 Hom.: 7288 Cov.: 32

Gnomad AFR AF: 0.0777

Gnomad AMI AF: 0.460

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.279 AC: 42447 AN: 152042 Hom.: 7284 Cov.: 32 AF XY: 0.274 AC XY: 20331 AN XY: 74276

Gnomad4 AFR AF: 0.0776

Gnomad4 AMR AF: 0.279

Gnomad4 ASJ AF: 0.299

Gnomad4 EAS AF: 0.247

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.301

Gnomad4 NFE AF: 0.394

Gnomad4 OTH AF: 0.321

Alfa AF: 0.290 Hom.: 1074

Bravo AF: 0.272

Asia WGS AF: 0.223 AC: 775 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.93
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs67807996; hg19: chr1-149995265;