rs7521902

chr1-22164231-C-Achr1-22164231-C-Gchr1-22164231-C-T

Variant summary

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

The XR_947057.3(LOC105376850):n.154+735C>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 0.222 in 152,158 control chromosomes in the GnomAD database, including 4,217 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 0.22 (4217 hom., cov: 32)
• Consequence: LOC105376850 XR_947057.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300

Genes affected

LOC105376850 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376850	XR_947057.3	n.154+735C>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33684 AN: 152040 Hom.: 4204 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.222 AC: 33722 AN: 152158 Hom.: 4217 Cov.: 32 AF XY: 0.229 AC XY: 17009 AN XY: 74384

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.507

Gnomad4 SAS AF: 0.336

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.230

Gnomad4 OTH AF: 0.204

Alfa AF: 0.219 Hom.: 2948

Bravo AF: 0.218

Asia WGS AF: 0.400 AC: 1388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	7.9
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7521902; hg19: chr1-22490724; COSMIC: COSV50192719;