rs7932639

Positions:

• chr11-38885620-G-A

Variant summary

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

The XR_001748189.1(LOC101928563):​n.1144C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0535 in 151,978 control chromosomes in the GnomAD database, including 519 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 0.054 (519 hom., cov: 32)
• Consequence: LOC101928563 XR_001748189.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0670

Genes affected

LOC101928563 (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 (EAS) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928563	XR_001748189.1	n.1144C>T		non_coding_transcript_exon_variant	1/6
LOC101928563	XR_001748190.2	n.1141C>T		non_coding_transcript_exon_variant	1/4
LOC101928563	XR_001748191.2	n.1150C>T		non_coding_transcript_exon_variant	1/6

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0534 AC: 8109 AN: 151860 Hom.: 517 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0220

Gnomad ASJ AF: 0.0124

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.0560

Gnomad FIN AF: 0.00747

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00755

Gnomad OTH AF: 0.0408

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

GnomAD4 genome AF: 0.0535 AC: 8134 AN: 151978 Hom.: 519 Cov.: 32 AF XY: 0.0533 AC XY: 3962 AN XY: 74274

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.0220

Gnomad4 ASJ AF: 0.0124

Gnomad4 EAS AF: 0.184

Gnomad4 SAS AF: 0.0560

Gnomad4 FIN AF: 0.00747

Gnomad4 NFE AF: 0.00755

Gnomad4 OTH AF: 0.0423

Alfa AF: 0.0226 Hom.: 47

Bravo AF: 0.0602

Asia WGS AF: 0.124 AC: 428 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7932639; hg19: chr11-38907170;