rs79811809

Variant names:

• chr7-140933681-A-G
• rs79811809
• XR_002956518.2:n.1531-5706A>G

Variant summary

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

The XR_002956518.2(LOC105375536):​n.1531-5706A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0607 in 152,270 control chromosomes in the GnomAD database, including 405 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 0.061 (405 hom., cov: 32)
• Consequence: LOC105375536 XR_002956518.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 2 publications found

Genes affected

LOC105375536 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0834 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: 0.0607 AC: 9236 AN: 152152 Hom.: 405 Cov.: 32

Gnomad AFR AF: 0.0152

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.0558

Gnomad ASJ AF: 0.0905

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0101

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0853

Gnomad OTH AF: 0.0597

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

GnomAD4 genome AF: 0.0607 AC: 9238 AN: 152270 Hom.: 405 Cov.: 32 AF XY: 0.0614 AC XY: 4571 AN XY: 74440

African (AFR) AF: 0.0152 AC: 632 AN: 41570

American (AMR) AF: 0.0558 AC: 853 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0905 AC: 314 AN: 3470

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5178

South Asian (SAS) AF: 0.0106 AC: 51 AN: 4830

European-Finnish (FIN) AF: 0.123 AC: 1300 AN: 10590

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0853 AC: 5800 AN: 68014

Other (OTH) AF: 0.0591 AC: 125 AN: 2116

Alfa AF: 0.0601 Hom.: 136

Bravo AF: 0.0534

Asia WGS AF: 0.00953 AC: 33 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.12
DANN	Benign	0.83
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs79811809; hg19: chr7-140633481;