chr8-72532428-T-C

Variant names:

• chr8-72532428-T-C
• rs349337
• XR_929042.3:n.732+217A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_929042.3(LOC105375897):​n.732+217A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0984 in 152,146 control chromosomes in the GnomAD database, including 852 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 0.098 (852 hom., cov: 32)
• Consequence: LOC105375897 XR_929042.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.614
• Publications: 2 publications found

Genes affected

LOC105375897 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0984 AC: 14955 AN: 152028 Hom.: 844 Cov.: 32

Gnomad AFR AF: 0.0966

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.0892

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.0992

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0845

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.0984 AC: 14977 AN: 152146 Hom.: 852 Cov.: 32 AF XY: 0.0993 AC XY: 7383 AN XY: 74380

African (AFR) AF: 0.0967 AC: 4014 AN: 41524

American (AMR) AF: 0.0890 AC: 1361 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 392 AN: 3472

East Asian (EAS) AF: 0.259 AC: 1343 AN: 5176

South Asian (SAS) AF: 0.153 AC: 737 AN: 4810

European-Finnish (FIN) AF: 0.0992 AC: 1050 AN: 10588

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0844 AC: 5739 AN: 67980

Other (OTH) AF: 0.106 AC: 224 AN: 2106

Alfa AF: 0.0895 Hom.: 842

Bravo AF: 0.0976

Asia WGS AF: 0.171 AC: 593 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.5
DANN	Benign	0.67
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs349337; hg19: chr8-73444663;