5-75312907-C-T

Variant names:

• chr5-75312907-C-T
• rs11957260
• XR_007058824.1:n.181+8043G>A

Variant summary

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

The XR_007058824.1(LOC124901007):​n.181+8043G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.575 in 151,506 control chromosomes in the GnomAD database, including 28,050 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 0.57 (28050 hom., cov: 30)
• Consequence: LOC124901007 XR_007058824.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 9 publications found

Genes affected

LOC124901007 (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 (AFR) allele frequency at 95% confidence interval = 0.883 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: 0.575 AC: 86997 AN: 151394 Hom.: 27993 Cov.: 30

Gnomad AFR AF: 0.890

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.575 AC: 87112 AN: 151506 Hom.: 28050 Cov.: 30 AF XY: 0.575 AC XY: 42535 AN XY: 73964

African (AFR) AF: 0.891 AC: 36847 AN: 41368

American (AMR) AF: 0.495 AC: 7537 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1822 AN: 3468

East Asian (EAS) AF: 0.527 AC: 2708 AN: 5138

South Asian (SAS) AF: 0.593 AC: 2854 AN: 4812

European-Finnish (FIN) AF: 0.457 AC: 4726 AN: 10334

Middle Eastern (MID) AF: 0.503 AC: 147 AN: 292

European-Non Finnish (NFE) AF: 0.427 AC: 28975 AN: 67868

Other (OTH) AF: 0.547 AC: 1145 AN: 2092

Alfa AF: 0.485 Hom.: 52870

Bravo AF: 0.588

Asia WGS AF: 0.588 AC: 2042 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	1.0
DANN	Benign	0.26
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs11957260; hg19: chr5-74608732;