rs7530302

Positions:

• chr1-220491610-G-A

Variant summary

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

The XR_001737822.1(LOC105372928):​n.557-624G>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 0.105 in 152,084 control chromosomes in the GnomAD database, including 1,175 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 0.10 (1175 hom., cov: 32)
• Consequence: LOC105372928 XR_001737822.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.20

Genes affected

LOC105372928 (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 = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372928	XR_001737822.1	n.557-624G>A		intron_variant, non_coding_transcript_variant
LOC105372928	XR_922615.1	n.256-624G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15893 AN: 151966 Hom.: 1166 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.0595

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.0334

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0591

Gnomad OTH AF: 0.0990

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

GnomAD4 genome AF: 0.105 AC: 15949 AN: 152084 Hom.: 1175 Cov.: 32 AF XY: 0.103 AC XY: 7672 AN XY: 74348

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.0593

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.0334

Gnomad4 NFE AF: 0.0591

Gnomad4 OTH AF: 0.102

Alfa AF: 0.0701 Hom.: 665

Bravo AF: 0.109

Asia WGS AF: 0.152 AC: 528 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	0.038
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7530302; hg19: chr1-220664952;