rs10979211

chr9-108108741-G-A

Variant summary

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

The XR_007061722.1(LOC105376214):n.721-55447C>T variant causes a intron, non coding transcript 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_007061722.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140

Genes affected

LOC105376214 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376214	XR_007061722.1	n.721-55447C>T		intron_variant, non_coding_transcript_variant
LOC105376214	XR_001746881.2	n.721-55447C>T		intron_variant, non_coding_transcript_variant
LOC105376214	XR_001746882.2	n.721-55447C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

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

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.0732

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.356

Gnomad4 OTH AF: 0.335

Alfa AF: 0.320 Hom.: 2596

Bravo AF: 0.300

Asia WGS AF: 0.232 AC: 806 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.18
Dann	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10979211; hg19: chr9-110871021;