7-110456628-A-G

Variant names:

• chr7-110456628-A-G
• rs396911
• XR_927862.3:n.594A>G

Variant summary

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

The XR_927862.3(LOC105375450):​n.594A>G 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 0.864 in 152,038 control chromosomes in the GnomAD database, including 56,904 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 0.86 (56904 hom., cov: 29)
• Consequence: LOC105375450 XR_927862.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400
• Publications: 5 publications found

Genes affected

LOC105375450 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.921 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375450	XR_927862.3	n.594A>G		non_coding_transcript_exon_variant	Exon 3 of 3
LOC105375451	XR_927863.3	n.291-23722T>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000226965	ENST00000435466.2	n.328-23722T>C		intron_variant	Intron 3 of 4	4
ENSG00000226965	ENST00000657059.1	n.438-23722T>C		intron_variant	Intron 1 of 2
ENSG00000226965	ENST00000658032.1	n.330+54432T>C		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.864 AC: 131251 AN: 151920 Hom.: 56860 Cov.: 29

Gnomad AFR AF: 0.929

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.905

Gnomad SAS AF: 0.856

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.840

Gnomad OTH AF: 0.850

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

GnomAD4 genome AF: 0.864 AC: 131357 AN: 152038 Hom.: 56904 Cov.: 29 AF XY: 0.863 AC XY: 64153 AN XY: 74330

African (AFR) AF: 0.929 AC: 38512 AN: 41470

American (AMR) AF: 0.820 AC: 12523 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.796 AC: 2762 AN: 3472

East Asian (EAS) AF: 0.905 AC: 4669 AN: 5158

South Asian (SAS) AF: 0.856 AC: 4122 AN: 4816

European-Finnish (FIN) AF: 0.836 AC: 8839 AN: 10576

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.840 AC: 57083 AN: 67970

Other (OTH) AF: 0.852 AC: 1792 AN: 2104

Alfa AF: 0.852 Hom.: 9227

Bravo AF: 0.864

Asia WGS AF: 0.866 AC: 3010 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	7.7
DANN	Benign	0.87
PhyloP100		-0.040

Splicing

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

Other links and lift over

dbSNP: rs396911; hg19: chr7-110096685;