rs11973012

Positions:

• chr7-127533608-T-C

Variant summary

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

The XR_007060511.1(LOC105375490):​n.174+1541A>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 0.0794 in 152,254 control chromosomes in the GnomAD database, including 575 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 0.079 (575 hom., cov: 32)
• Consequence: LOC105375490 XR_007060511.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.945

Genes affected

LOC105375490 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0983 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375490	XR_007060511.1	n.174+1541A>G		intron_variant, non_coding_transcript_variant
LOC105375490	XR_001745351.2	n.2291+1541A>G		intron_variant, non_coding_transcript_variant
LOC105375490	XR_001745352.2	n.493+1541A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0795 AC: 12092 AN: 152136 Hom.: 575 Cov.: 32

Gnomad AFR AF: 0.0331

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0729

Gnomad ASJ AF: 0.0545

Gnomad EAS AF: 0.0948

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.0746

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

GnomAD4 genome AF: 0.0794 AC: 12089 AN: 152254 Hom.: 575 Cov.: 32 AF XY: 0.0806 AC XY: 6001 AN XY: 74442

Gnomad4 AFR AF: 0.0331

Gnomad4 AMR AF: 0.0729

Gnomad4 ASJ AF: 0.0545

Gnomad4 EAS AF: 0.0944

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.100

Gnomad4 OTH AF: 0.0734

Alfa AF: 0.0876 Hom.: 99

Bravo AF: 0.0727

Asia WGS AF: 0.0980 AC: 343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
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: rs11973012; hg19: chr7-127173662;