XR_007096271.1:n.283+5748C>A

Variant names:

• chr3-104543865-G-T
• rs2961177
• XR_007096271.1:n.283+5748C>A

Variant summary

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

The XR_007096271.1(LOC105374021):​n.283+5748C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.983 in 152,310 control chromosomes in the GnomAD database, including 73,634 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 0.98 (73634 hom., cov: 32)
• Consequence: LOC105374021 XR_007096271.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.623
• Publications: 2 publications found

Genes affected

LOC105374021 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.983 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.983 AC: 149607 AN: 152192 Hom.: 73579 Cov.: 32

Gnomad AFR AF: 0.991

Gnomad AMI AF: 0.998

Gnomad AMR AF: 0.991

Gnomad ASJ AF: 0.993

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.897

Gnomad FIN AF: 0.995

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.987

Gnomad OTH AF: 0.984

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

GnomAD4 genome AF: 0.983 AC: 149717 AN: 152310 Hom.: 73634 Cov.: 32 AF XY: 0.982 AC XY: 73093 AN XY: 74470

African (AFR) AF: 0.991 AC: 41203 AN: 41570

American (AMR) AF: 0.991 AC: 15152 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.993 AC: 3447 AN: 3472

East Asian (EAS) AF: 0.890 AC: 4609 AN: 5176

South Asian (SAS) AF: 0.897 AC: 4332 AN: 4828

European-Finnish (FIN) AF: 0.995 AC: 10576 AN: 10624

Middle Eastern (MID) AF: 0.966 AC: 284 AN: 294

European-Non Finnish (NFE) AF: 0.987 AC: 67133 AN: 68032

Other (OTH) AF: 0.979 AC: 2071 AN: 2116

Alfa AF: 0.988 Hom.: 3432

Bravo AF: 0.985

Asia WGS AF: 0.883 AC: 3069 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.29
DANN	Benign	0.40
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs2961177; hg19: chr3-104262709;