chr11-38885620-G-A

Variant names:

• chr11-38885620-G-A
• rs7932639
• XR_001748189.1:n.1144C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

LOC101928563 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC101928563	XR_001748189.1	n.1144C>T		non_coding_transcript_exon_variant	Exon 1 of 6
LOC101928563	XR_001748190.2	n.1141C>T		non_coding_transcript_exon_variant	Exon 1 of 4
LOC101928563	XR_001748191.2	n.1150C>T		non_coding_transcript_exon_variant	Exon 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285751	ENST00000722718.1	n.439-6260C>T		intron_variant	Intron 2 of 5

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

African (AFR) AF: 0.141 AC: 5843 AN: 41468

American (AMR) AF: 0.0220 AC: 335 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.0124 AC: 43 AN: 3466

East Asian (EAS) AF: 0.184 AC: 948 AN: 5164

South Asian (SAS) AF: 0.0560 AC: 270 AN: 4820

European-Finnish (FIN) AF: 0.00747 AC: 79 AN: 10580

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.00755 AC: 513 AN: 67922

Other (OTH) AF: 0.0423 AC: 89 AN: 2106

Alfa AF: 0.0229 Hom.: 59

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
PhyloP100		-0.067

Splicing

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

Other links and lift over

dbSNP: rs7932639; hg19: chr11-38907170;