rs7950640

Positions:

• chr11-59096932-G-C
• chr11-59096932-G-T

Variant summary

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

The XR_001748221.3(LOC105369315):​n.4562-22C>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 0.451 in 152,072 control chromosomes in the GnomAD database, including 15,768 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 0.45 (15768 hom., cov: 32)
• Consequence: LOC105369315 XR_001748221.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900

Genes affected

LOC105369315 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105369315	XR_001748221.3	n.4562-22C>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68495 AN: 151954 Hom.: 15758 Cov.: 32

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.451 AC: 68541 AN: 152072 Hom.: 15768 Cov.: 32 AF XY: 0.453 AC XY: 33701 AN XY: 74342

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.533

Gnomad4 ASJ AF: 0.393

Gnomad4 EAS AF: 0.347

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.482

Gnomad4 NFE AF: 0.414

Gnomad4 OTH AF: 0.470

Alfa AF: 0.281 Hom.: 637

Bravo AF: 0.458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.59
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7950640; hg19: chr11-58864405;