rs721608

Positions:

• chr11-57230449-A-G

Variant summary

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

The XR_007062670.1(LOC105369309):​n.244-228T>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 0.285 in 152,050 control chromosomes in the GnomAD database, including 6,757 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 0.29 (6757 hom., cov: 31)
• Consequence: LOC105369309 XR_007062670.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131

Genes affected

LOC105369309 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369309	XR_007062670.1	n.244-228T>C		intron_variant, non_coding_transcript_variant
LOC105369309	XR_001748217.1	n.244-228T>C		intron_variant, non_coding_transcript_variant
LOC105369309	XR_007062671.1	n.244-228T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43334 AN: 151932 Hom.: 6760 Cov.: 31

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.285 AC: 43340 AN: 152050 Hom.: 6757 Cov.: 31 AF XY: 0.279 AC XY: 20709 AN XY: 74310

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.188

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.372

Gnomad4 OTH AF: 0.276

Alfa AF: 0.349 Hom.: 4502

Bravo AF: 0.279

Asia WGS AF: 0.206 AC: 720 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.7
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs721608; hg19: chr11-56997923;