rs10979211

Variant names:

• chr9-108108741-G-A
• rs10979211
• XR_001746881.2:n.721-55447C>T

Variant summary

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

The XR_001746881.2(LOC105376214):​n.721-55447C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 152,052 control chromosomes in the GnomAD database, including 7,600 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 0.31 (7600 hom., cov: 32)
• Consequence: LOC105376214 XR_001746881.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140
• Publications: 0 publications found

Genes affected

LOC105376214 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.352 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: 0.307 AC: 46637 AN: 151934 Hom.: 7602 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.0734

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.307 AC: 46652 AN: 152052 Hom.: 7600 Cov.: 32 AF XY: 0.304 AC XY: 22555 AN XY: 74306

African (AFR) AF: 0.247 AC: 10227 AN: 41480

American (AMR) AF: 0.299 AC: 4563 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 882 AN: 3470

East Asian (EAS) AF: 0.0732 AC: 378 AN: 5164

South Asian (SAS) AF: 0.357 AC: 1716 AN: 4806

European-Finnish (FIN) AF: 0.313 AC: 3306 AN: 10578

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.356 AC: 24207 AN: 67970

Other (OTH) AF: 0.335 AC: 705 AN: 2104

Alfa AF: 0.329 Hom.: 4396

Bravo AF: 0.300

Asia WGS AF: 0.232 AC: 806 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.18
DANN	Benign	0.24
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs10979211; hg19: chr9-110871021;